diff --git a/auth/MANIFEST.in b/auth/MANIFEST.in
index 16688ad841a..fe8d7b8c4df 100644
--- a/auth/MANIFEST.in
+++ b/auth/MANIFEST.in
@@ -1 +1,2 @@
 recursive-include auth/templates *
+recursive-include auth/static *
diff --git a/auth/auth/auth.py b/auth/auth/auth.py
index a5447aabd74..d176a719a20 100644
--- a/auth/auth/auth.py
+++ b/auth/auth/auth.py
@@ -9,6 +9,7 @@
 from urllib.parse import urlparse
 
 import aiohttp_session
+import jinja2
 import kubernetes_asyncio.client
 import kubernetes_asyncio.client.rest
 import kubernetes_asyncio.config
@@ -67,6 +68,8 @@
 
 CLOUD = get_global_config()['cloud']
 DEFAULT_NAMESPACE = os.environ['HAIL_DEFAULT_NAMESPACE']
+INACTIVE_USER_TIMEOUT_DAYS = int(os.environ.get('INACTIVE_USER_TIMEOUT_DAYS', '60'))
+AUTH_ROOT = os.path.dirname(os.path.abspath(__file__))
 
 is_test_deployment = DEFAULT_NAMESPACE != 'default'
 
@@ -219,9 +222,7 @@ def validate_next_page_url(next_page):
     actual_next_page_domain = urlparse(next_page).netloc
 
     if actual_next_page_domain not in valid_next_domains:
-        raise web.HTTPBadRequest(
-            text=f'Invalid next page: \'{next_page}\'. Domain \'{actual_next_page_domain}\' not in {valid_next_domains}'
-        )
+        raise web.HTTPBadRequest(text='Invalid next page.')
 
 
 @routes.get('/healthcheck')
@@ -243,6 +244,22 @@ async def openapi(request):
     return await render_template('auth', request, None, 'openapi.yaml', page_context)
 
 
+@routes.get('/auth/static/js/{filename}')
+@web_security_headers
+async def fetch_js_file(request):
+    filename = request.match_info['filename']
+    if filename.endswith('.js'):
+        page_context = {'base_path': deploy_config.base_path('auth')}
+        try:
+            response = await render_template('auth', request, None, f'js/{filename}', page_context)
+            response.content_type = 'application/javascript'
+            return response
+        except jinja2.exceptions.TemplateNotFound as error:
+            raise web.HTTPNotFound() from error
+    else:
+        raise web.HTTPNotFound()
+
+
 @routes.get('')
 @routes.get('/')
 @web_security_headers
@@ -271,7 +288,12 @@ async def creating_account(request: web.Request, userdata: Optional[UserData]) -
             set_message(session, f'Account does not exist for login id {login_id}.', 'error')
             raise web.HTTPFound(deploy_config.external_url('auth', ''))
 
-        page_context = {'username': user['username'], 'state': user['state'], 'login_id': user['login_id']}
+        page_context = {
+            'username': user['username'],
+            'state': user['state'],
+            'login_id': user['login_id'],
+            'inactive_timeout_days': INACTIVE_USER_TIMEOUT_DAYS,
+        }
 
         if user['state'] in ('deleting', 'deleted'):
             return await render_template('auth', request, userdata, 'account-error.html', page_context)
@@ -422,9 +444,16 @@ async def callback(request) -> web.Response:
 
         raise web.HTTPFound(creating_url)
 
-    if user['state'] in ('deleting', 'deleted'):
-        page_context = {'username': user['username'], 'state': user['state'], 'login_id': user['login_id']}
-        return await render_template('auth', request, user, 'account-error.html', page_context)
+    if user['state'] in ('deleting', 'deleted', 'inactive'):
+        page_context = {
+            'username': user['username'],
+            'state': user['state'],
+            'login_id': user['login_id'],
+            'inactive_timeout_days': INACTIVE_USER_TIMEOUT_DAYS,
+        }
+        return await render_template(
+            'auth', request, user, 'account-error.html', page_context, status_code=web.HTTPUnauthorized.status_code
+        )
 
     if user['state'] == 'creating':
         if caller == 'signup':
@@ -1239,7 +1268,7 @@ def run():
         ]
     )
 
-    setup_aiohttp_jinja2(app, 'auth')
+    setup_aiohttp_jinja2(app, 'auth', jinja2.FileSystemLoader(f'{AUTH_ROOT}/static/'))
     setup_aiohttp_session(app)
 
     setup_common_static_routes(routes)
diff --git a/auth/auth/static/js/account-creating.js b/auth/auth/static/js/account-creating.js
new file mode 100644
index 00000000000..ea518d93414
--- /dev/null
+++ b/auth/auth/static/js/account-creating.js
@@ -0,0 +1,5 @@
+let protocol = location.protocol.replace("http", "ws")
+let sock = new WebSocket(protocol + location.host + "{{ base_path }}/creating/wait");
+sock.onmessage = function (_event) {
+    window.location.reload()
+}
diff --git a/auth/auth/static/js/roles.js b/auth/auth/static/js/roles.js
new file mode 100644
index 00000000000..36a5cd63577
--- /dev/null
+++ b/auth/auth/static/js/roles.js
@@ -0,0 +1,73 @@
+const csrfToken = document.head.querySelector('meta[name="csrf"]')?.getAttribute('value') || '';
+
+document.getElementsByName('remove-role-button').forEach(button => {
+        button.addEventListener('click', (_e) => { removeRole(button.dataset.user, button.dataset.role); })
+});
+
+document.getElementsByName('add-role-button').forEach(button => {
+        button.addEventListener('click', (_e) => { addRole(button.dataset['username-input-id'], button.dataset.role); })
+});
+
+async function removeRole(username, roleName) {
+    if (!confirm(`Are you sure you want to remove the '${roleName}' role from user '${username}'?`)) {
+        return;
+    }
+
+    try {
+        const response = await fetch("{{ base_path }}/api/v1alpha/system_roles/${username}", {
+            method: 'PATCH',
+            headers: {
+                'Content-Type': 'application/json',
+                'X-CSRF-Token': csrfToken
+            },
+            body: JSON.stringify({
+                role_removal: roleName
+            })
+        });
+
+        if (response.ok) {
+            // Refresh the page to show updated data
+            window.location.reload();
+        } else {
+            const errorData = await response.json().catch(() => ({}));
+            alert(`Failed to remove role: ${errorData.message || response.statusText}`);
+        }
+    } catch (error) {
+        console.error('Error removing role:', error);
+        alert('Failed to remove role. Please try again.');
+    }
+}
+
+async function addRole(usernameInputId, roleName) {
+    const username = document.getElementById(usernameInputId).value.trim();
+
+    if (!username) {
+        alert('Please enter a username');
+        return;
+    }
+
+    try {
+        const response = await fetch("{{ base_path }}/api/v1alpha/system_roles/${username}", {
+            method: 'PATCH',
+            headers: {
+                'Content-Type': 'application/json',
+                'X-CSRF-Token': csrfToken
+            },
+            body: JSON.stringify({
+                role_addition: roleName
+            })
+        });
+
+        if (response.ok) {
+            // Clear the input and refresh the page
+            document.getElementById(usernameInputId).value = '';
+            window.location.reload();
+        } else {
+            const errorData = await response.json().catch(() => ({}));
+            alert(`Failed to add role: ${errorData.message || response.statusText}`);
+        }
+    } catch (error) {
+        console.error('Error adding role:', error);
+        alert('Failed to add role. Please try again.');
+    }
+}
diff --git a/auth/auth/static/js/user.js b/auth/auth/static/js/user.js
new file mode 100644
index 00000000000..2d9298b9d1a
--- /dev/null
+++ b/auth/auth/static/js/user.js
@@ -0,0 +1,23 @@
+const tosCheckbox = document.getElementById('tosCheckbox');
+tosCheckbox.addEventListener('load', (_e) => { updateButtons(); })
+tosCheckbox.addEventListener('change', (_e) => { updateButtons(); })
+
+function updateButtons() {
+    const checkbox = document.getElementById('tosCheckbox');
+    const signupButton = document.getElementById('signupButton');
+    const loginButton = document.getElementById('loginButton');
+
+    signupButton.disabled = !checkbox.checked;
+    loginButton.disabled = !checkbox.checked;
+
+    // Update button styles based on state
+    [signupButton, loginButton].forEach(button => {
+        if (button.disabled) {
+            button.classList.add('opacity-50', 'cursor-not-allowed');
+            button.classList.remove('hover:bg-blue-700');
+        } else {
+            button.classList.remove('opacity-50', 'cursor-not-allowed');
+            button.classList.add('hover:bg-blue-700');
+        }
+    });
+}
diff --git a/auth/auth/static/js/users.js b/auth/auth/static/js/users.js
new file mode 100644
index 00000000000..ebee6818611
--- /dev/null
+++ b/auth/auth/static/js/users.js
@@ -0,0 +1,35 @@
+const showActiveCheckbox = document.getElementById('show-active');
+showActiveCheckbox.addEventListener('change', (_e) => { filterTable(); })
+const showDevelopersCheckbox = document.getElementById('show-developers');
+showDevelopersCheckbox.addEventListener('change', (_e) => { filterTable(); })
+
+const reactivateUserForm = document.getElementById('reactivate-user-form');
+reactivateUserForm.addEventListener('submit', (_e) => { validateReactivateForm(); })
+
+function filterTable() {
+    const showActive = document.getElementById('show-active').checked;
+    const showDevelopers = document.getElementById('show-developers').checked;
+
+    const rows = document.querySelectorAll('#users-table tbody tr');
+
+    rows.forEach(row => {
+        const state = row.querySelector('[data-state]').dataset.state.trim();
+        const isDeveloper = row.querySelector('[data-developer]').dataset.developer.trim();
+
+        let show = true;
+        if (showActive && state !== 'active') show = false;
+        if (showDevelopers && isDeveloper !== '1') show = false;
+
+        row.style.display = show ? '' : 'none';
+    });
+}
+function validateReactivateForm() {
+    const userId = document.getElementById('inactive-id').value.trim();
+    const username = document.getElementById('inactive-username').value.trim();
+
+    if (!userId && !username) {
+        alert('Please provide either a User ID or a Username.');
+        return false;
+    }
+    return true;
+}
diff --git a/auth/auth/templates/account-creating.html b/auth/auth/templates/account-creating.html
index e4fad1f0d4a..45dd8308aa7 100644
--- a/auth/auth/templates/account-creating.html
+++ b/auth/auth/templates/account-creating.html
@@ -5,11 +5,7 @@
   <div class="spinner"></div>
   <b>Creating account for {{ username }}</b>
 </div>
-<script>
-  let protocol = location.protocol.replace("http", "ws")
-  let sock = new WebSocket(protocol + location.host + "{{ base_path }}/creating/wait");
-  sock.onmessage = function (event) {
-      window.location.reload()
-  }
+
+<script defer src='{{ auth_base_url }}/auth/static/js/account-creating.js'>
 </script>
 {% endblock %}
diff --git a/auth/auth/templates/account-error.html b/auth/auth/templates/account-error.html
index b7845aaa6e4..e9e53ea4a1e 100644
--- a/auth/auth/templates/account-error.html
+++ b/auth/auth/templates/account-error.html
@@ -2,14 +2,33 @@
 {% block title %}Account Error{% endblock %}
 {% block content %}
 <div class="vcentered">
- <div><b>Account is in a bad state!</b></div>
+{% if state == 'inactive' %}
+  <div><b>Your account is inactive</b></div>
   <br>
   <div>
-    Please contact <a href="mailto:hail-team@broadinstitute.org">hail-team@broadinstitute.org</a>
+    Accounts that haven't been logged into for {{ inactive_timeout_days }} days are automatically marked as inactive.
+    <br>
+    {% if support_email %}
+    Contact <a href="mailto:{{ support_email }}?subject=Reactivate%20account%3A%20{{ username | urlencode }}&body=Hello%2C%0A%0APlease%20reactivate%20my%20Hail%20account.%0A%0AUsername%3A%20{{ username | urlencode }}%0ALogin%20ID%3A%20{{ login_id | urlencode }}%0A%0AThank%20you" class="text-sky-600 underline hover:text-sky-800 font-medium">{{ support_email }}</a> to reactivate.
+    {% else %}
+    Contact contact your support team to reactivate.
+    {% endif %}
+  </div>
+{% else %}
+  <div><b>Account is in a bad state!</b></div>
+  <br>
+  <div>
+    {% if support_email %}
+    Please contact <a href="mailto:{{ support_email }}" class="text-sky-600 underline hover:text-sky-800 font-medium">{{ support_email }}</a> to get help.
+    {% else %}
+    Please contact your support team to get help.
+    {% endif %}
     <br>
-    <div class="small">Username: <b>{{ username }}</b></div>
-    <div class="small">Login ID: <b>{{ login_id }}</b></div>
     <div class="small">State: <b>{{ state }}</b></div>
   </div>
+{% endif %}
+  <br>
+  <div class="small">Username: <b>{{ username }}</b></div>
+  <div class="small">Login ID: <b>{{ login_id }}</b></div>
 </div>
 {% endblock %}
diff --git a/auth/auth/templates/roles.html b/auth/auth/templates/roles.html
index 676cb81664c..da460aa4695 100644
--- a/auth/auth/templates/roles.html
+++ b/auth/auth/templates/roles.html
@@ -1,8 +1,11 @@
 {% extends "layout.html" %}
 {% block title %}Roles{% endblock %}
+{% block head %}
+    <meta name="csrf" value="{{ csrf_token }}" />
+{% endblock %}
 {% block content %}
 
-{% if all_system_role_assignments.keys().__len__() > 0 %}
+{% if all_system_role_assignments.keys().__len__() >= 0 %}
 <h1 class='text-2xl font-light mb-4'>System role assignments</h1>
 
 <table class='table-auto w-full border border-slate-300 border-collapse font-inter'>
@@ -28,8 +31,10 @@ <h1 class='text-2xl font-light mb-4'>System role assignments</h1>
         <ul class='list-none pl-0'>
           {% for user in all_system_role_assignments[role]['users'] %}
           <li class='flex items-center mb-1'>
-            <button 
-              onclick="removeRole('{{ user }}', '{{ role }}')"
+            <button
+              name='remove-role-button'
+              data-user='{{ user }}'
+              data-role='{{ role }}'
               class='mr-2 w-6 flex-shrink-0 text-red-600 hover:text-red-800 transition-colors duration-200 flex items-center justify-center'
               title='Remove {{ role }} role from {{ user }}'
             >
@@ -48,16 +53,18 @@ <h1 class='text-2xl font-light mb-4'>System role assignments</h1>
               <path fill-rule='evenodd' d='M10 5a1 1 0 011 1v3h3a1 1 0 110 2h-3v3a1 1 0 11-2 0v-3H6a1 1 0 110-2h3V6a1 1 0 011-1z' clip-rule='evenodd'/>
             </svg>
           </span>
-          <input 
-            type='text' 
+          <input
+            type='text'
             id='add-user-{{ role }}'
             placeholder='Enter username'
             autocomplete='off'
             data-lpignore='true'
             class='flex-1 border border-slate-300 rounded px-2 py-1 text-sm mr-2'
           />
-          <button 
-            onclick="addRole('{{ role }}')"
+          <button
+            name='add-role-button'
+            data-role='{{ role }}'
+            data-username-input-id="add-user-{{ role }}"
             class='bg-blue-600 text-white px-3 py-1 rounded text-sm hover:bg-blue-700 transition-colors duration-200'
             title='Add {{ role }} role to user'
           >
@@ -69,72 +76,7 @@ <h1 class='text-2xl font-light mb-4'>System role assignments</h1>
     {% endfor %}
   </tbody>
 </table>
-{% endif %}
-
-<script>
-async function removeRole(username, roleName) {
-  if (!confirm(`Are you sure you want to remove the '${roleName}' role from user '${username}'?`)) {
-    return;
-  }
-
-  try {
-    const response = await fetch(`{{ base_path }}/api/v1alpha/system_roles/${username}`, {
-      method: 'PATCH',
-      headers: {
-        'Content-Type': 'application/json',
-        'X-CSRF-Token': '{{ csrf_token }}'
-      },
-      body: JSON.stringify({
-        role_removal: roleName
-      })
-    });
 
-    if (response.ok) {
-      // Refresh the page to show updated data
-      window.location.reload();
-    } else {
-      const errorData = await response.json().catch(() => ({}));
-      alert(`Failed to remove role: ${errorData.message || response.statusText}`);
-    }
-  } catch (error) {
-    console.error('Error removing role:', error);
-    alert('Failed to remove role. Please try again.');
-  }
-}
-
-async function addRole(roleName) {
-  const inputId = `add-user-${roleName}`;
-  const username = document.getElementById(inputId).value.trim();
-  
-  if (!username) {
-    alert('Please enter a username');
-    return;
-  }
-
-  try {
-    const response = await fetch(`{{ base_path }}/api/v1alpha/system_roles/${username}`, {
-      method: 'PATCH',
-      headers: {
-        'Content-Type': 'application/json',
-        'X-CSRF-Token': '{{ csrf_token }}'
-      },
-      body: JSON.stringify({
-        role_addition: roleName
-      })
-    });
-
-    if (response.ok) {
-      // Clear the input and refresh the page
-      document.getElementById(inputId).value = '';
-      window.location.reload();
-    } else {
-      const errorData = await response.json().catch(() => ({}));
-      alert(`Failed to add role: ${errorData.message || response.statusText}`);
-    }
-  } catch (error) {
-    console.error('Error adding role:', error);
-    alert('Failed to add role. Please try again.');
-  }
-}
-</script>
+<script defer src='{{ auth_base_url }}/auth/static/js/roles.js'></script>
+{% endif %}
 {% endblock %}
diff --git a/auth/auth/templates/user.html b/auth/auth/templates/user.html
index cb0d98a911f..d1222c71f17 100644
--- a/auth/auth/templates/user.html
+++ b/auth/auth/templates/user.html
@@ -32,10 +32,10 @@ <h1 class='text-4xl mb-4'>Log in to continue</h1>
   {% else %}
     <p>You must sign up or log in to continue</p>
   {% endif %}
-  
+
   <div class="mb-4">
     <label class="flex items-center">
-      <input type="checkbox" id="tosCheckbox" class="mr-2" onchange="updateButtons()">
+      <input type="checkbox" id="tosCheckbox" class="mr-2">
       <span>I have reviewed and agree to the <a href="https://batch.hail.is/tos" target="_blank" class="text-blue-600 hover:underline">Terms of Service</a>
         and have read the <a href="https://batch.hail.is/privacy" target="_blank" class="text-blue-600 hover:underline">Privacy Policy</a>
       </span>
@@ -63,30 +63,7 @@ <h1 class='text-4xl mb-4'>Log in to continue</h1>
     </div>
   </div>
 
-  <script>
-    function updateButtons() {
-      const checkbox = document.getElementById('tosCheckbox');
-      const signupButton = document.getElementById('signupButton');
-      const loginButton = document.getElementById('loginButton');
-      
-      signupButton.disabled = !checkbox.checked;
-      loginButton.disabled = !checkbox.checked;
-      
-      // Update button styles based on state
-      [signupButton, loginButton].forEach(button => {
-        if (button.disabled) {
-          button.classList.add('opacity-50', 'cursor-not-allowed');
-          button.classList.remove('hover:bg-blue-700');
-        } else {
-          button.classList.remove('opacity-50', 'cursor-not-allowed');
-          button.classList.add('hover:bg-blue-700');
-        }
-      });
-    }
-
-    // Initialize button states
-    updateButtons();
-  </script>
+  <script defer src="{{ auth_base_url }}/auth/static/js/user.js"></script>
   {% endif %}
 
   <p>
diff --git a/auth/auth/templates/users.html b/auth/auth/templates/users.html
index 88fc7e7383e..7e2baf60006 100644
--- a/auth/auth/templates/users.html
+++ b/auth/auth/templates/users.html
@@ -37,7 +37,7 @@ <h1 class='text-2xl font-light mb-4'>Create User</h1>
   </div>
   <div class='w-full md:w-2/5'>
     <h1 class='text-2xl font-light mb-4'>Reactivate User</h1>
-    <form action="{{ base_path }}/users/activate" method="POST" onsubmit="validateReactivateForm()">
+    <form action="{{ base_path }}/users/activate" method="POST" id="reactivate-user-form">
       <div class='flex-col space-y-2'>
         <div class='flex items-center space-x-4'>
           <span class='w-32'>User ID</span>
@@ -93,11 +93,11 @@ <h1 class='text-2xl font-light mb-4'>Invalidate All User Sessions</h1>
 <h1 class='text-2xl font-light mb-4'>Users</h1>
 <div class="mb-4 flex space-x-4">
   <label class="inline-flex items-center">
-    <input type="checkbox" id="show-active" class="form-checkbox" onchange="filterTable()">
+    <input type="checkbox" id="show-active" class="form-checkbox">
     <span class="ml-2">Only Active</span>
   </label>
   <label class="inline-flex items-center">
-    <input type="checkbox" id="show-developers" class="form-checkbox" onchange="filterTable()">
+    <input type="checkbox" id="show-developers" class="form-checkbox">
     <span class="ml-2">Only Developers</span>
   </label>
 </div>
@@ -130,33 +130,5 @@ <h1 class='text-2xl font-light mb-4'>Users</h1>
   </tbody>
 </table>
 
-<script>
-function filterTable() {
-  const showActive = document.getElementById('show-active').checked;
-  const showDevelopers = document.getElementById('show-developers').checked;
-
-  const rows = document.querySelectorAll('#users-table tbody tr');
-
-  rows.forEach(row => {
-    const state = row.querySelector('[data-state]').dataset.state.trim();
-    const isDeveloper = row.querySelector('[data-developer]').dataset.developer.trim();
-
-    let show = true;
-    if (showActive && state !== 'active') show = false;
-    if (showDevelopers && isDeveloper !== '1') show = false;
-
-    row.style.display = show ? '' : 'none';
-  });
-}
-function validateReactivateForm() {
-  const userId = document.getElementById('inactive-id').value.trim();
-  const username = document.getElementById('inactive-username').value.trim();
-
-  if (!userId && !username) {
-    alert('Please provide either a User ID or a Username.');
-    return false;
-  }
-  return true;
-}
-</script>
+<script defer src="{{auth_base_url}}/auth/static/js/users.js"></script>
 {% endblock %}
diff --git a/auth/deployment.yaml b/auth/deployment.yaml
index 955c5b63fac..a8460358657 100644
--- a/auth/deployment.yaml
+++ b/auth/deployment.yaml
@@ -198,6 +198,12 @@ spec:
                 key: cloud
           - name: HAIL_SHA
             value: "{{ code.sha }}"
+          - name: INACTIVE_USER_TIMEOUT_DAYS
+            valueFrom:
+              secretKeyRef:
+                name: auth-config
+                key: inactive_user_timeout_days
+                optional: true
 {% if scope != "test" %}
           - name: HAIL_SHOULD_PROFILE
             value: "1"
diff --git a/batch/batch/batch_configuration.py b/batch/batch/batch_configuration.py
index b1d1e77e373..d153d15c53d 100644
--- a/batch/batch/batch_configuration.py
+++ b/batch/batch/batch_configuration.py
@@ -8,6 +8,7 @@
 CLOUD = os.environ['CLOUD']
 DOCKER_ROOT_IMAGE = os.environ['HAIL_DOCKER_ROOT_IMAGE']
 DOCKER_PREFIX = os.environ['HAIL_DOCKER_PREFIX']
+DOCKERHUB_PREFIX = os.environ.get('HAIL_DOCKERHUB_PREFIX', '')
 
 KUBERNETES_SERVER_URL = os.environ['KUBERNETES_SERVER_URL']
 INTERNAL_GATEWAY_IP = os.environ['INTERNAL_GATEWAY_IP']
diff --git a/batch/batch/cloud/gcp/driver/create_instance.py b/batch/batch/cloud/gcp/driver/create_instance.py
index 1580b95ab94..b18c7da6082 100644
--- a/batch/batch/cloud/gcp/driver/create_instance.py
+++ b/batch/batch/cloud/gcp/driver/create_instance.py
@@ -129,7 +129,7 @@ def scheduling() -> dict:
                 'network': 'global/networks/default',
                 'subnetwork': f'regions/{region}/subnetworks/default',
                 'networkTier': 'PREMIUM',
-                'accessConfigs': [{'type': 'ONE_TO_ONE_NAT', 'name': 'external-nat'}],
+                'stackType': 'IPV4_ONLY',
             }
         ],
         'scheduling': scheduling(),
diff --git a/batch/batch/driver/instance_collection/job_private.py b/batch/batch/driver/instance_collection/job_private.py
index c33fe5c9d8f..7164761af94 100644
--- a/batch/batch/driver/instance_collection/job_private.py
+++ b/batch/batch/driver/instance_collection/job_private.py
@@ -199,19 +199,21 @@ async def schedule_jobs_loop_body(self):
             batch_id = record['batch_id']
             job_id = record['job_id']
             instance_name = record['instance_name']
-            id = (batch_id, job_id)
-            log.info(f'scheduling job {id}')
+            log.info(f'scheduling job {(batch_id, job_id)}')
 
             instance = self.name_instance[instance_name]
             n_records_seen += 1
 
-            async def schedule_with_error_handling(app, record, id, instance):
+            async def schedule_with_error_handling(app, record, instance):
                 try:
                     await schedule_job(app, record, instance)
                 except Exception:
-                    log.info(f'scheduling job {id} on {instance} for {self}', exc_info=True)
+                    log.info(
+                        f'scheduling job {(record["batch_id"], record["job_id"])} on {instance} for {self}',
+                        exc_info=True,
+                    )
 
-            await waitable_pool.call(schedule_with_error_handling, self.app, record, id, instance)
+            await waitable_pool.call(schedule_with_error_handling, self.app, record, instance)
 
         await waitable_pool.wait()
 
@@ -427,13 +429,14 @@ async def user_runnable_jobs(user, remaining) -> AsyncIterator[Dict[str, Any]]:
             async for record in user_runnable_jobs(user, remaining):
                 batch_id = record['batch_id']
                 job_id = record['job_id']
-                id = (batch_id, job_id)
                 attempt_id = secret_alnum_string(6)
                 record['attempt_id'] = attempt_id
                 job_group_id = record['job_group_id']
                 n_prior_attempts = record['n_prior_attempts']
                 n_max_attempts = record['n_max_attempts']
-                log.info(f'Job {id}: {n_prior_attempts} prior attempts out of a maximum of {n_max_attempts}')
+                log.info(
+                    f'Job {(batch_id, job_id)}: {n_prior_attempts} prior attempts out of a maximum of {n_max_attempts}'
+                )
 
                 if n_prior_attempts >= n_max_attempts:
                     await mark_job_errored(
@@ -459,10 +462,10 @@ async def user_runnable_jobs(user, remaining) -> AsyncIterator[Dict[str, Any]]:
                 n_user_instances_created += 1
                 should_wait = False
 
-                log.info(f'creating job private instance for job {id}')
+                log.info(f'creating job private instance for job {(batch_id, job_id)}')
 
                 async def create_instance_with_error_handling(
-                    batch_id: int, job_id: int, attempt_id: str, job_group_id: int, record: dict, id: Tuple[int, int]
+                    batch_id: int, job_id: int, attempt_id: str, job_group_id: int, record: dict
                 ):
                     try:
                         batch_format_version = BatchFormatVersion(record['format_version'])
@@ -493,10 +496,12 @@ async def create_instance_with_error_handling(
                             traceback.format_exc(),
                         )
                     except Exception:
-                        log.exception(f'while creating job private instance for job {id}', exc_info=True)
+                        log.exception(
+                            f'while creating job private instance for job {(batch_id, job_id)}', exc_info=True
+                        )
 
                 await waitable_pool.call(
-                    create_instance_with_error_handling, batch_id, job_id, attempt_id, job_group_id, record, id
+                    create_instance_with_error_handling, batch_id, job_id, attempt_id, job_group_id, record
                 )
 
                 remaining.value -= 1
diff --git a/batch/batch/driver/instance_collection/pool.py b/batch/batch/driver/instance_collection/pool.py
index a1b5391f373..95e6313fda0 100644
--- a/batch/batch/driver/instance_collection/pool.py
+++ b/batch/batch/driver/instance_collection/pool.py
@@ -709,7 +709,9 @@ async def user_runnable_jobs(user):
 
                 n_prior_attempts = record['n_prior_attempts']
                 n_max_attempts = record['n_max_attempts']
-                log.info(f'Job {id}: {n_prior_attempts} prior attempts out of a maximum of {n_max_attempts}')
+                log.info(
+                    f'Job {(record["batch_id"], record["job_id"])}: {n_prior_attempts} prior attempts out of a maximum of {n_max_attempts}'
+                )
 
                 if n_prior_attempts >= n_max_attempts:
                     await mark_job_errored(
diff --git a/batch/batch/driver/main.py b/batch/batch/driver/main.py
index 1291c90f727..a66d32ceaae 100644
--- a/batch/batch/driver/main.py
+++ b/batch/batch/driver/main.py
@@ -93,6 +93,8 @@
 
 log.info(f'REFRESH_INTERVAL_IN_SECONDS {REFRESH_INTERVAL_IN_SECONDS}')
 
+DRIVER_ROOT = os.path.dirname(os.path.abspath(__file__))
+
 routes = web.RouteTableDef()
 
 deploy_config = get_deploy_config()
@@ -580,12 +582,13 @@ async def configure_feature_flags(request: web.Request, _) -> NoReturn:
 
     compact_billing_tables = 'compact_billing_tables' in post
     oms_agent = 'oms_agent' in post
+    dockerhub_proxy = 'dockerhub_proxy' in post
 
     await db.execute_update(
         """
-UPDATE feature_flags SET compact_billing_tables = %s, oms_agent = %s;
+UPDATE feature_flags SET compact_billing_tables = %s, oms_agent = %s, dockerhub_proxy = %s;
 """,
-        (compact_billing_tables, oms_agent),
+        (compact_billing_tables, oms_agent, dockerhub_proxy),
     )
 
     row = await db.select_and_fetchone('SELECT * FROM feature_flags')
@@ -1792,6 +1795,7 @@ def run():
 
     setup_aiohttp_jinja2(app, 'batch.driver')
     setup_common_static_routes(routes)
+    routes.static('/batch_driver/static/js', f'{DRIVER_ROOT}/static/js')
     app.add_routes(routes)
     app.router.add_get("/metrics", server_stats)
 
diff --git a/batch/batch/driver/static/js/quotas.js b/batch/batch/driver/static/js/quotas.js
new file mode 100644
index 00000000000..6fd91163110
--- /dev/null
+++ b/batch/batch/driver/static/js/quotas.js
@@ -0,0 +1,6 @@
+if (Object.hasOwn(window, "Plotly")) {
+    if (document.getElementById('plotly-timeseries') !== undefined) {
+        var graphJson = JSON.parse(document.getElementById('plotly-timeseries').dataset.graph);
+        window.Plotly.plot('plotly-timeseries', graphJson, {});
+    }
+}
diff --git a/batch/batch/driver/templates/index.html b/batch/batch/driver/templates/index.html
index db10e46cc97..21ca75b794b 100644
--- a/batch/batch/driver/templates/index.html
+++ b/batch/batch/driver/templates/index.html
@@ -41,6 +41,12 @@ <h1>Feature Flags</h1>
              name="oms_agent"
              {% if feature_flags['oms_agent'] %}checked{% endif %}
       value="true" />
+      <label for="dockerhub_proxy">dockerhub_proxy: </label>
+      <input type="checkbox"
+             id="dockerhub_proxy"
+             name="dockerhub_proxy"
+             {% if feature_flags['dockerhub_proxy'] %}checked{% endif %}
+      value="true" />
       <div>
         <button>Update</button>
       </div>
diff --git a/batch/batch/driver/templates/quotas.html b/batch/batch/driver/templates/quotas.html
index 84fbb1264b2..ee3185d3ed7 100644
--- a/batch/batch/driver/templates/quotas.html
+++ b/batch/batch/driver/templates/quotas.html
@@ -4,13 +4,10 @@
 
 <h1>Quotas by Region</h1>
 {% if plot_json is not none %}
+<div id="plotly-timeseries" data-graph='{{ plot_json | safe}}'></div>
 <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
-<div id="plotly-timeseries">
-    <script>
-        var graph = {{ plot_json | safe }};
-        Plotly.plot('plotly-timeseries', graph, {});
-    </script>
-</div>
+<script defer src="{{ base_path }}/batch_driver/static/js/quotas.js"></script>
+
 <style>
     .header-dropdown {
         display: block;
diff --git a/batch/batch/front_end/front_end.py b/batch/batch/front_end/front_end.py
index 259f2a1bae7..f4f2283cf01 100644
--- a/batch/batch/front_end/front_end.py
+++ b/batch/batch/front_end/front_end.py
@@ -19,6 +19,7 @@
 import aiohttp.web_exceptions
 import aiohttp_session
 import humanize
+import jinja2
 import pandas as pd
 import plotly
 import plotly.express as px
@@ -82,7 +83,7 @@
 )
 
 from ..batch import batch_record_to_dict, cancel_job_group_in_db, job_group_record_to_dict, job_record_to_dict
-from ..batch_configuration import BATCH_STORAGE_URI, CLOUD, DEFAULT_NAMESPACE, SCOPE
+from ..batch_configuration import BATCH_STORAGE_URI, CLOUD, DEFAULT_NAMESPACE, DOCKERHUB_PREFIX, SCOPE
 from ..batch_format_version import BatchFormatVersion
 from ..cloud.azure.resource_utils import azure_cores_mcpu_to_memory_bytes
 from ..cloud.gcp.resource_utils import GCP_MACHINE_FAMILY, gcp_cores_mcpu_to_memory_bytes
@@ -117,6 +118,7 @@
     query_billing_projects_with_cost,
     query_billing_projects_without_cost,
     regions_to_bits_rep,
+    rewrite_dockerhub_image,
     unavailable_if_frozen,
 )
 from .query import (
@@ -145,6 +147,8 @@
 
 auth = get_authenticator()
 
+FRONT_END_ROOT = os.path.dirname(__file__)
+
 BATCH_JOB_DEFAULT_CPU = os.environ.get('HAIL_BATCH_JOB_DEFAULT_CPU', '1')
 BATCH_JOB_DEFAULT_MEMORY = os.environ.get('HAIL_BATCH_JOB_DEFAULT_MEMORY', 'standard')
 BATCH_JOB_DEFAULT_STORAGE = os.environ.get('HAIL_BATCH_JOB_DEFAULT_STORAGE', '0Gi')
@@ -1406,6 +1410,18 @@ async def _create_jobs(
         if machine_type and pool_label:
             raise web.HTTPBadRequest(reason='cannot specify pool label with machine_type')
 
+        # Rewrite Docker Hub images if feature flag is enabled
+        if (
+            spec['process']['type'] == 'docker'
+            and DOCKERHUB_PREFIX
+            and app['feature_flags'].get('dockerhub_proxy', False)
+        ):
+            original_image = spec['process']['image']
+            rewritten_image = rewrite_dockerhub_image(original_image, DOCKERHUB_PREFIX)
+            if rewritten_image is not None:
+                spec['process']['image'] = rewritten_image
+                log.info(f'Rewrote Docker Hub image {original_image} to {rewritten_image} for job {batch_id}/{job_id}')
+
         if spec['process']['type'] == 'jvm':
             jvm_requested_cpu = parse_cpu_in_mcpu(resources.get('cpu', BATCH_JOB_DEFAULT_CPU))
             if 'cpu' in resources and jvm_requested_cpu not in (1000, 2000, 4000, 8000):
@@ -3707,6 +3723,22 @@ async def privacy(request):
     return await render_template('batch', request, None, 'privacy.html', {})
 
 
+@routes.get('/batch/static/js/{filename}')
+@web_security_headers
+async def fetch_js_file(request):
+    filename = request.match_info['filename']
+    if filename.endswith('.js'):
+        page_context = {'base_path': deploy_config.base_path('batch')}
+        try:
+            response = await render_template('batch', request, None, f'js/{filename}', page_context)
+            response.content_type = 'application/javascript'
+            return response
+        except jinja2.exceptions.TemplateNotFound as error:
+            raise web.HTTPNotFound() from error
+    else:
+        raise web.HTTPNotFound()
+
+
 async def cancel_batch_loop_body(app):
     client_session = app[CommonAiohttpAppKeys.CLIENT_SESSION]
     await retry_transient_errors(
@@ -3791,6 +3823,9 @@ async def on_startup(app):
 
     app['frozen'] = row['frozen']
 
+    row = await db.select_and_fetchone('SELECT * FROM feature_flags')
+    app['feature_flags'] = row
+
     regions: Dict[str, int] = {
         record['region']: record['region_id']
         async for record in db.select_and_fetchall('SELECT region_id, region from regions')
@@ -3856,7 +3891,7 @@ def run():
     )
     setup_aiohttp_session(app)
 
-    setup_aiohttp_jinja2(app, 'batch.front_end')
+    setup_aiohttp_jinja2(app, 'batch.front_end', jinja2.FileSystemLoader(f'{FRONT_END_ROOT}/static/'))
     setup_common_static_routes(routes)
     app.add_routes(routes)
     app.router.add_get("/metrics", server_stats)
diff --git a/batch/batch/front_end/query/query_v2.py b/batch/batch/front_end/query/query_v2.py
index 2eba30a95fa..34a0fdddfa0 100644
--- a/batch/batch/front_end/query/query_v2.py
+++ b/batch/batch/front_end/query/query_v2.py
@@ -294,7 +294,7 @@ def parse_job_group_jobs_query_v2(
         attempts_table_join_str = ''
 
     sql = f"""
-SELECT jobs.*, batches.user, batches.billing_project, batches.format_version, job_attributes.value AS name, cost_t.cost,
+SELECT STRAIGHT_JOIN jobs.*, batches.user, batches.billing_project, batches.format_version, job_attributes.value AS name, cost_t.cost,
   cost_t.cost_breakdown
 FROM jobs
 INNER JOIN batches ON jobs.batch_id = batches.id
diff --git a/batch/batch/front_end/static/js/auto_refresh.js b/batch/batch/front_end/static/js/auto_refresh.js
new file mode 100644
index 00000000000..45426426922
--- /dev/null
+++ b/batch/batch/front_end/static/js/auto_refresh.js
@@ -0,0 +1,28 @@
+(function () {
+    var container = document.getElementById('auto-refresh');
+    if (!container) return;
+
+    var detail = document.getElementById('auto-refresh-detail');
+    var checkbox = document.getElementById('auto-refresh-toggle');
+    var timer = null;
+
+    function scheduleRefresh() {
+        var target = new Date(Date.now() + 60000);
+        detail.textContent = '(at ' + target.toLocaleTimeString() + ')';
+        timer = setTimeout(function () {
+            location.reload();
+        }, 60000);
+    }
+
+    checkbox.addEventListener('change', function () {
+        if (checkbox.checked) {
+            scheduleRefresh();
+        } else {
+            clearTimeout(timer);
+            timer = null;
+            detail.textContent = '(every minute)';
+        }
+    });
+
+    scheduleRefresh();
+})();
diff --git a/batch/batch/front_end/static/js/job.js b/batch/batch/front_end/static/js/job.js
new file mode 100644
index 00000000000..c606d300bdf
--- /dev/null
+++ b/batch/batch/front_end/static/js/job.js
@@ -0,0 +1,11 @@
+if (Object.hasOwn(window, "Plotly")) {
+    if (document.getElementById('plotly-job-durations') != null) {
+        var durationGraph = JSON.parse(document.getElementById('plotly-job-durations').dataset.graph);
+        window.Plotly.plot('plotly-job-durations', durationGraph, {});
+    }
+
+    if (document.getElementById('plotly-job-resource-usage') != null) {
+        var resourceUsageGraph = JSON.parse(document.getElementById('plotly-job-resource-usage').dataset.graph);
+        window.Plotly.plot('plotly-job-resource-usage', resourceUsageGraph, {});
+    }
+}
diff --git a/batch/batch/front_end/static/js/table_search.js b/batch/batch/front_end/static/js/table_search.js
new file mode 100644
index 00000000000..dd2643723b7
--- /dev/null
+++ b/batch/batch/front_end/static/js/table_search.js
@@ -0,0 +1,386 @@
+document.getElementsByName("table-search-input-box").forEach(input => {
+    input.addEventListener("keydown", function (e) {
+        if (e.key === "Enter" && (e.metaKey || e.ctrlKey)) {
+            e.preventDefault();
+            var formId = input.id.substring(0, input.id.lastIndexOf("-input-box")) + "-form";
+            document.getElementById(formId).submit();
+        }
+    })
+});
+
+// Field configurations with their allowed operators and value types
+const fieldConfigs = {
+    // General fields
+    'name': {
+        operators: ['=', '!=', '=~', '!~'],
+        type: 'string',
+        placeholder: 'Enter name...'
+    },
+    'cost': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'number',
+        placeholder: 'Enter cost (e.g., 5.00)...'
+    },
+    'duration': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'number',
+        placeholder: 'Enter duration in seconds...'
+    },
+    'start_time': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'datetime',
+        placeholder: 'Enter date (ISO format, e.g., 2025-02-27T17:15:25Z)...'
+    },
+    'end_time': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'datetime',
+        placeholder: 'Enter date (ISO format, e.g., 2025-02-27T17:15:25Z)...'
+    },
+    'state': {
+        operators: ['=', '!='],
+        type: 'string',
+        placeholder: 'Select state...'
+    },
+
+    // Batch-specific fields
+    'batch_id': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'number',
+        placeholder: 'Enter batch ID...'
+    },
+    'user': {
+        operators: ['=', '!='],
+        type: 'string',
+        placeholder: 'Enter username...'
+    },
+    'billing_project': {
+        operators: ['=', '!='],
+        type: 'string',
+        placeholder: 'Enter billing project...'
+    },
+
+    // Job-specific fields
+    'job_id': {
+        operators: ['=', '!=', '>', '>=', '<', '<='],
+        type: 'number',
+        placeholder: 'Enter job ID...'
+    },
+    'instance': {
+        operators: ['=', '!=', '=~', '!~'],
+        type: 'string',
+        placeholder: 'Enter instance name...'
+    },
+    'instance_collection': {
+        operators: ['=', '!=', '=~', '!~'],
+        type: 'string',
+        placeholder: 'Enter instance collection...'
+    }
+};
+
+// Special state values
+const stateValues = {
+    batch: ['running', 'complete', 'success', 'failure', 'cancelled', 'open', 'closed'],
+    job: ['pending', 'ready', 'creating', 'running', 'live', 'cancelled', 'error', 'failed', 'bad', 'success', 'done']
+};
+
+// Global variable for search context
+let isJobSearch;
+let currentMode = 'dropdown'; // 'dropdown' or 'textbox'
+
+// Update operators based on selected field
+function updateOperators(selectElement) {
+    const field = selectElement.value;
+    const operatorSelect = selectElement.parentElement.querySelector('.operator-select');
+    const valueInput = selectElement.parentElement.querySelector('.value-input');
+
+    // Clear existing options
+    operatorSelect.innerHTML = '<option value="">Select operator...</option>';
+
+    if (field && Object.hasOwn(fieldConfigs, field)) {
+        const config = fieldConfigs[field];
+
+        // Add operator options
+        config.operators.forEach(op => {
+            const option = document.createElement('option');
+            option.value = op;
+            option.textContent = op;
+            operatorSelect.appendChild(option);
+        });
+
+        // Update value input
+        valueInput.placeholder = config.placeholder;
+
+        // Handle state fields via dropdown
+        if (field === 'state') {
+            valueInput.style.display = 'none';
+            if (!selectElement.parentElement.querySelector('.state-select')) {
+                const stateSelect = document.createElement('select');
+                stateSelect.className = 'state-select p-2 bg-white rounded border';
+                stateSelect.innerHTML = '<option value="">Select state...</option>';
+
+                const values = isJobSearch ? stateValues.job : stateValues.batch;
+                values.forEach(state => {
+                    const option = document.createElement('option');
+                    option.value = state;
+                    option.textContent = state;
+                    stateSelect.appendChild(option);
+                });
+
+                valueInput.parentElement.insertBefore(stateSelect, valueInput);
+            }
+        } else {
+            valueInput.style.display = 'block';
+            const stateSelect = selectElement.parentElement.querySelector('.state-select');
+            if (stateSelect) {
+                stateSelect.remove();
+            }
+        }
+    }
+}
+
+// Add new search criterion
+function addCriterion() {
+    const container = document.getElementById('search-criteria-container');
+    const newCriterion = container.querySelector('.search-criterion').cloneNode(true);
+
+    // Reset values
+    newCriterion.querySelector('.criterion-select').value = '';
+    newCriterion.querySelector('.criterion-select').addEventListener('change', function (_e) { updateOperators(this); });
+    newCriterion.querySelector('.operator-select').innerHTML = '<option value="">Select operator...</option>';
+    newCriterion.querySelector('.value-input').value = '';
+    newCriterion.querySelector('.value-input').placeholder = 'Enter value...';
+    newCriterion.querySelector('.remove-criterion').addEventListener('click', function (_e) { removeCriterion(this); });
+
+    // Remove any state select
+    const stateSelect = newCriterion.querySelector('.state-select');
+    if (stateSelect) {
+        stateSelect.remove();
+    }
+
+    container.appendChild(newCriterion);
+    updateRemoveButtonsVisibility(container);
+}
+
+// Update visibility of remove buttons based on criteria count
+function updateRemoveButtonsVisibility(container) {
+    const criteria = container.querySelectorAll('.search-criterion');
+    const removeButtons = container.querySelectorAll('.remove-criterion');
+
+    removeButtons.forEach(button => {
+        if (criteria.length <= 1) {
+            button.style.display = 'none';
+        } else {
+            button.style.display = 'block';
+        }
+    });
+}
+
+// Remove search criterion
+function removeCriterion(button) {
+    const container = button.closest('[id$="-criteria-container"]');
+    const criteria = container.querySelectorAll('.search-criterion');
+
+    // Don't remove if it's the last criterion
+    if (criteria.length > 1) {
+        button.closest('.search-criterion').remove();
+        updateRemoveButtonsVisibility(container);
+    }
+}
+
+// Build query string from criteria
+function buildQuery() {
+    const container = document.getElementById('search-criteria-container');
+    const criteria = container.querySelectorAll('.search-criterion');
+    const queryParts = [];
+
+    criteria.forEach(criterion => {
+        const field = criterion.querySelector('.criterion-select').value;
+        const operator = criterion.querySelector('.operator-select').value;
+        let value = criterion.querySelector('.value-input').value;
+
+        // Check for state select
+        const stateSelect = criterion.querySelector('.state-select');
+        if (stateSelect && stateSelect.style.display !== 'none') {
+            value = stateSelect.value;
+        }
+
+        if (field && operator && value) {
+            queryParts.push(`${field} ${operator} ${value}`);
+        }
+    });
+
+    return queryParts.join('\n');
+}
+
+// Parse existing query and populate dropdowns
+function parseQuery(query) {
+    if (!query) return;
+
+    const container = document.getElementById('search-criteria-container');
+    const existingCriteria = container.querySelectorAll('.search-criterion');
+
+    // Remove extra criteria, keeping only the first one
+    for (let i = Number(existingCriteria.length - 1); i > 0; i--) {
+        existingCriteria[i].remove();
+    }
+
+    const lines = query.split('\n').filter(line => line.trim());
+
+    lines.forEach((line, index) => {
+        let criterion;
+
+        if (index === 0) {
+            // Use the existing first criterion
+            criterion = container.querySelector('.search-criterion');
+        } else {
+            // Add additional criteria
+            addCriterion();
+            const criteria = container.querySelectorAll('.search-criterion');
+            criterion = criteria[criteria.length - 1];
+        }
+
+        // Parse line and populate the criterion
+        const parts = line.trim().match(/^(\w+)\s*(=~|!~|<=|>=|!=|==|=|<|>)\s*(.+)$/);
+
+        if (parts && criterion) {
+            const [, field, operator, value] = parts;
+
+            criterion.querySelector('.criterion-select').value = field;
+            updateOperators(criterion.querySelector('.criterion-select'));
+            criterion.querySelector('.operator-select').value = operator;
+
+            if (field === 'state') {
+                const stateSelect = criterion.querySelector('.state-select');
+                if (stateSelect) {
+                    stateSelect.value = value;
+                }
+            } else {
+                criterion.querySelector('.value-input').value = value;
+            }
+        }
+    });
+
+    updateRemoveButtonsVisibility(container);
+}
+
+// Toggle between dropdown and textbox input modes
+function toggleInputMode() {
+    const dropdownContainer = document.getElementById('search-criteria-container');
+    const textboxContainer = document.getElementById('search-textbox-container');
+    const toggleButton = document.getElementById('search-toggle-mode');
+    const addButton = document.getElementById('search-add-criterion');
+    const textbox = document.getElementById('search-input-box');
+    const hiddenInput = document.getElementById('search-query');
+
+    if (currentMode === 'dropdown') {
+        // Switch to textbox mode and sync dropdown to textbox
+        const query = buildQuery();
+        textbox.value = query;
+        hiddenInput.value = query;
+
+        dropdownContainer.style.display = 'none';
+        textboxContainer.style.display = 'block';
+        toggleButton.textContent = 'Switch to drop-down query input';
+        addButton.style.display = 'none';
+
+        currentMode = 'textbox';
+    } else {
+        // Switch to dropdown mode and sync textbox to dropdown
+        const query = textbox.value.trim();
+        hiddenInput.value = query;
+
+        dropdownContainer.style.display = 'block';
+        textboxContainer.style.display = 'none';
+        toggleButton.textContent = 'Switch to textbox query input';
+        addButton.style.display = 'block';
+
+        // Parse the textbox query back into dropdowns
+        if (query) {
+            parseQuery(query);
+        } else {
+            // If textbox is empty, reset to single empty criterion
+            const container = document.getElementById('search-criteria-container');
+            const criteria = container.querySelectorAll('.search-criterion');
+            // Remove extra criteria, keep only first one
+            for (let i = criteria.length - 1; i > 0; i--) {
+                criteria[i].remove();
+            }
+            // Reset first criterion
+            const firstCriterion = container.querySelector('.search-criterion');
+            if (firstCriterion) {
+                firstCriterion.querySelector('.criterion-select').value = '';
+                firstCriterion.querySelector('.operator-select').innerHTML = '<option value="">Select operator...</option>';
+                firstCriterion.querySelector('.value-input').value = '';
+                const stateSelect = firstCriterion.querySelector('.state-select');
+                if (stateSelect) stateSelect.remove();
+            }
+            updateRemoveButtonsVisibility(container);
+        }
+
+        currentMode = 'dropdown';
+    }
+
+    // Add real-time sync for textbox changes
+    if (currentMode === 'textbox') {
+        // Remove previous listener if any, then add
+        textbox.removeEventListener('input', syncTextboxToHiddenInput);
+        textbox.addEventListener('input', syncTextboxToHiddenInput);
+    }
+}
+// Handler for syncing textbox to hidden input
+function syncTextboxToHiddenInput() {
+    const hiddenInput = document.getElementById('search-query');
+    const textbox = document.getElementById('search-input-box');
+    hiddenInput.value = textbox.value;
+}
+
+// Form submission handler
+document.getElementById('search-form').addEventListener('submit', function(_e) {
+    let query;
+    if (currentMode === 'dropdown') {
+        query = buildQuery();
+    } else {
+        query = document.getElementById('search-input-box').value;
+    }
+    document.getElementById('search-query').value = query;
+});
+
+// Initialize on page load
+document.addEventListener('DOMContentLoaded', function() {
+    // Initialize search context
+    isJobSearch = document.getElementById('search-form').getAttribute('data-is-job-search') === 'true';
+
+    const container = document.getElementById('search-criteria-container');
+    const existingQuery = document.getElementById('search-query').value;
+    if (existingQuery) {
+        parseQuery(existingQuery);
+    } else {
+        // Update remove button visibility on initial load
+        updateRemoveButtonsVisibility(container);
+    }
+});
+
+// Keyboard shortcut support
+document.addEventListener("keydown", function (e) {
+    if (e.key === "Enter" && (e.metaKey || e.ctrlKey)) {
+        e.preventDefault();
+        let query;
+        if (currentMode === 'dropdown') {
+            query = buildQuery();
+        } else {
+            query = document.getElementById('search-input-box').value;
+        }
+        document.getElementById('search-query').value = query;
+        document.getElementById('search-form').submit();
+    }
+});
+
+// Add initial event listeners
+document.getElementsByName('remove-criterion').forEach(button => {
+    button.addEventListener('click', function (_e) { removeCriterion(this) });
+} );
+document.getElementsByName('criterion-select').forEach(selector => {
+    selector.addEventListener('change', function (_e) { updateOperators(this) });
+} );
+document.getElementById('search-add-criterion').addEventListener('click', _e => addCriterion());
+document.getElementById('search-toggle-mode').addEventListener('click', _e => toggleInputMode());
diff --git a/batch/batch/front_end/templates/batch.html b/batch/batch/front_end/templates/batch.html
index 9895b5949db..20e0bcfac95 100644
--- a/batch/batch/front_end/templates/batch.html
+++ b/batch/batch/front_end/templates/batch.html
@@ -1,12 +1,13 @@
 {% from "table_search.html" import table_search with context %}
 {% from "components/metadata_tables.html" import kv_table, resource_cost_table, collapsible_li, job_status_table %}
 {% from "utils.html" import
-batch_state_indicator, job_state_indicator, danger_button, submit_button, link
+batch_state_indicator, job_state_indicator, danger_button, submit_button, link, auto_refresh
 %}
 {% extends "layout.html" %}
 {% block title %}Batch {{ batch['id'] }}{% endblock %}
 {% block head %}
-<script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+<script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+<script defer src="{{ base_path }}/batch/static/js/auto_refresh.js"></script>
 {% endblock %}
 {% block content %}
 <div class='flex flex-wrap justify-around pt-8 gap-y-4'>
@@ -22,6 +23,9 @@
           {{ batch['attributes']['name'] }}
           {% endif %}
         </div>
+        {% if not batch['complete'] %}
+        {{ auto_refresh() }}
+        {% endif %}
         <div class='flex justify-between items-center'>
           <div>
             <div class='font-light text-zinc-500'>Submitted by {{ batch['user'] }}</div>
diff --git a/batch/batch/front_end/templates/batches.html b/batch/batch/front_end/templates/batches.html
index 095c6605554..c27787dfcfd 100644
--- a/batch/batch/front_end/templates/batches.html
+++ b/batch/batch/front_end/templates/batches.html
@@ -3,7 +3,7 @@
 {% extends "layout.html" %}
 {% block title %}Batches{% endblock %}
 {% block head %}
-<script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+<script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 {% block content %}
 <div class='flex-col m-auto w-full space-y-4'>
diff --git a/batch/batch/front_end/templates/job.html b/batch/batch/front_end/templates/job.html
index 44d29803e75..f5eb9635f89 100644
--- a/batch/batch/front_end/templates/job.html
+++ b/batch/batch/front_end/templates/job.html
@@ -1,5 +1,5 @@
 {% from "components/metadata_tables.html" import collapsible_li, resource_cost_table, kv_table %}
-{% from "utils.html" import success_check, fail_cross, progress_spinner, job_state_indicator %}
+{% from "utils.html" import success_check, fail_cross, progress_spinner, job_state_indicator, auto_refresh %}
 {% extends "layout.html" %}
 {% block title %}Batch {{ batch_id }} Job {{ job_id }}{% endblock %}
 
@@ -84,6 +84,9 @@ <h4 class='text-xl font-light'>Logs</h4>
           {{ job['attributes']['name'] }}
           {% endif %}
         </div>
+        {% if job['state'] not in ('Success', 'Failed', 'Error', 'Cancelled') %}
+        {{ auto_refresh() }}
+        {% endif %}
         <div class='flex justify-between'>
           <div>
             <div class='font-light text-zinc-500'>Submitted by {{ job['user'] }}</div>
@@ -128,7 +131,7 @@ <h4 class='text-xl font-light'>Logs</h4>
       {% endif %}
 
       {% if plot_job_durations is not none %}
-      <div id="plotly-job-durations"></div>
+      <div data-graph='{{plot_job_durations | safe }}' id="plotly-job-durations"></div>
       {% endif %}
     </div>
   </div>
@@ -160,7 +163,7 @@ <h2 class='text-2xl font-light mx-4 my-3'>Attempts</h2>
   {% if plot_resource_usage is not none %}
   <div class='relative overflow-hidden transition-all bg-white'>
     <div class='w-full overflow-auto flex justify-center'>
-      <div id="plotly-job-resource-usage"></div>
+      <div data-graph='{{plot_resource_usage | safe }}' id="plotly-job-resource-usage"></div>
     </div>
   </div>
   {% endif %}
@@ -231,18 +234,9 @@ <h3 class='text-xl font-light py-2'>Command</h3>
   </div>
   {% endif %}
 </div>
-{% if plot_job_durations is not none %}
+<script defer src="{{ base_path }}/batch/static/js/auto_refresh.js"></script>
+{% if plot_job_durations is not none or plot_resource_usage is not none %}
 <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
-<script>
-  var graph = {{plot_job_durations | safe }};
-  Plotly.plot('plotly-job-durations', graph, {});
-</script>
-{% endif %}
-{% if plot_resource_usage is not none %}
-<script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
-<script>
-  var graph = {{plot_resource_usage | safe }};
-  Plotly.plot('plotly-job-resource-usage', graph, {});
-</script>
+<script defer src="{{ base_path }}/batch/static/js/job.js"></script>
 {% endif %}
 {% endblock %}
diff --git a/batch/batch/front_end/templates/table_search.html b/batch/batch/front_end/templates/table_search.html
index 1d733a61f8d..2d68938e8c4 100644
--- a/batch/batch/front_end/templates/table_search.html
+++ b/batch/batch/front_end/templates/table_search.html
@@ -3,13 +3,13 @@
 <!-- Determine search context based on component_name (see table search, in batches.html and batch.html) -->
 {% set is_job_search = component_name == "job-search" %}
 
-<form id='{{ component_name }}-form' class='min-h-48 flex space-x-4' method="GET" action="{{ endpoint }}" data-is-job-search="{{ 'true' if is_job_search else 'false' }}">
+<form id='search-form' class='min-h-48 flex space-x-4' method="GET" action="{{ endpoint }}" data-is-job-search="{{ 'true' if is_job_search else 'false' }}">
   <div class='basis-2/3'>
     <!-- Search criteria container -->
-    <div id='{{ component_name }}-criteria-container' class='min-h-24 w-full p-4 bg-slate-200 rounded space-y-3'>
+    <div id='search-criteria-container' class='min-h-24 w-full p-4 bg-slate-200 rounded space-y-3'>
       <!-- Initial search criterion -->
       <div class='search-criterion flex space-x-2 items-center'>
-        <select class='criterion-select p-2 bg-white rounded border' onchange='updateOperators(this)'>
+        <select name='criterion-select' class='criterion-select p-2 bg-white rounded border'>
           <option value="">Select a field...</option>
           <optgroup label="General">
             <option value="name">Name</option>
@@ -41,25 +41,25 @@
 
         <input type='text' class='value-input p-2 bg-white rounded border flex-grow' placeholder='Enter value...'>
 
-        <button type='button' class='remove-criterion text-red-500 hover:text-red-700' onclick='removeCriterion(this)' title='Remove criterion'>
+        <button type='button' name='remove-criterion' class='remove-criterion text-red-500 hover:text-red-700' title='Remove criterion'>
           <span class="material-symbols-outlined text-sm">close</span>
         </button>
       </div>
     </div>
 
     <!-- Textbox mode (hidden by default) -->
-    <div id='{{ component_name }}-textbox-container' class='min-h-32 w-full p-4 bg-slate-200 rounded' style='display: none;'>
-      <textarea id='{{ component_name }}-input-box' class='h-32 w-full p-4 bg-white rounded resize whitespace-pre border'
+    <div id='search-textbox-container' class='min-h-32 w-full p-4 bg-slate-200 rounded' style='display: none;'>
+      <textarea id='search-input-box' class='h-32 w-full p-4 bg-white rounded resize whitespace-pre border'
         spellcheck="false" autocorrect="off" placeholder='Enter search query (e.g., "cost > 5.00")'>{% if q %}{{ q }}{% endif %}</textarea>
     </div>
 
     <!-- Buttons below search box container -->
     <div class='flex justify-between items-center mt-3'>
       <div class='flex space-x-2'>
-        <button type='button' id='{{ component_name }}-add-criterion' class='px-3 py-1 bg-blue-500 text-white rounded text-sm hover:bg-blue-600' onclick='addCriterion("{{ component_name }}")'>
+        <button type='button' id='search-add-criterion' class='px-3 py-1 bg-blue-500 text-white rounded text-sm hover:bg-blue-600'>
           Add Search Criterion
         </button>
-        <button type='button' id='{{ component_name }}-toggle-mode' class='px-3 py-1 bg-gray-500 text-white rounded text-sm hover:bg-gray-600' onclick='toggleInputMode("{{ component_name }}")'>
+        <button type='button' id='search-toggle-mode' class='px-3 py-1 bg-gray-500 text-white rounded text-sm hover:bg-gray-600'>
           Switch to textbox query input
         </button>
       </div>
@@ -67,7 +67,7 @@
     </div>
 
     <!-- Hidden input to store the built query -->
-    <input type='hidden' id='{{ component_name }}-query' name='q' value='{% if q %}{{ q }}{% endif %}'>
+    <input type='hidden' id='search-query' name='q' value='{% if q %}{{ q }}{% endif %}'>
   </div>
 
   <div class='flex items-start'>
@@ -77,370 +77,5 @@
   </div>
 </form>
 
-<script>
-// Field configurations with their allowed operators and value types
-const fieldConfigs = {
-  // General fields
-  'name': {
-    operators: ['=', '!=', '=~', '!~'],
-    type: 'string',
-    placeholder: 'Enter name...'
-  },
-  'cost': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'number',
-    placeholder: 'Enter cost (e.g., 5.00)...'
-  },
-  'duration': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'number',
-    placeholder: 'Enter duration in seconds...'
-  },
-  'start_time': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'datetime',
-    placeholder: 'Enter date (ISO format, e.g., 2025-02-27T17:15:25Z)...'
-  },
-  'end_time': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'datetime',
-    placeholder: 'Enter date (ISO format, e.g., 2025-02-27T17:15:25Z)...'
-  },
-  'state': {
-    operators: ['=', '!='],
-    type: 'string',
-    placeholder: 'Select state...'
-  },
-
-  // Batch-specific fields
-  'batch_id': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'number',
-    placeholder: 'Enter batch ID...'
-  },
-  'user': {
-    operators: ['=', '!='],
-    type: 'string',
-    placeholder: 'Enter username...'
-  },
-  'billing_project': {
-    operators: ['=', '!='],
-    type: 'string',
-    placeholder: 'Enter billing project...'
-  },
-
-  // Job-specific fields
-  'job_id': {
-    operators: ['=', '!=', '>', '>=', '<', '<='],
-    type: 'number',
-    placeholder: 'Enter job ID...'
-  },
-  'instance': {
-    operators: ['=', '!=', '=~', '!~'],
-    type: 'string',
-    placeholder: 'Enter instance name...'
-  },
-  'instance_collection': {
-    operators: ['=', '!=', '=~', '!~'],
-    type: 'string',
-    placeholder: 'Enter instance collection...'
-  }
-};
-
-// Special state values
-const stateValues = {
-  batch: ['running', 'complete', 'success', 'failure', 'cancelled', 'open', 'closed'],
-  job: ['pending', 'ready', 'creating', 'running', 'live', 'cancelled', 'error', 'failed', 'bad', 'success', 'done']
-};
-
-// Global variable for search context
-let isJobSearch;
-let currentMode = 'dropdown'; // 'dropdown' or 'textbox'
-
-// Update operators based on selected field
-function updateOperators(selectElement) {
-  const field = selectElement.value;
-  const operatorSelect = selectElement.parentElement.querySelector('.operator-select');
-  const valueInput = selectElement.parentElement.querySelector('.value-input');
-
-  // Clear existing options
-  operatorSelect.innerHTML = '<option value="">Select operator...</option>';
-
-  if (field && fieldConfigs[field]) {
-    const config = fieldConfigs[field];
-
-    // Add operator options
-    config.operators.forEach(op => {
-      const option = document.createElement('option');
-      option.value = op;
-      option.textContent = op;
-      operatorSelect.appendChild(option);
-    });
-
-    // Update value input
-    valueInput.placeholder = config.placeholder;
-
-    // Handle state fields via dropdown
-    if (field === 'state') {
-      valueInput.style.display = 'none';
-      if (!selectElement.parentElement.querySelector('.state-select')) {
-        const stateSelect = document.createElement('select');
-        stateSelect.className = 'state-select p-2 bg-white rounded border';
-        stateSelect.innerHTML = '<option value="">Select state...</option>';
-
-        const values = isJobSearch ? stateValues.job : stateValues.batch;
-        values.forEach(state => {
-          const option = document.createElement('option');
-          option.value = state;
-          option.textContent = state;
-          stateSelect.appendChild(option);
-        });
-
-        valueInput.parentElement.insertBefore(stateSelect, valueInput);
-      }
-    } else {
-      valueInput.style.display = 'block';
-      const stateSelect = selectElement.parentElement.querySelector('.state-select');
-      if (stateSelect) {
-        stateSelect.remove();
-      }
-    }
-  }
-}
-
-// Add new search criterion
-function addCriterion(componentName) {
-  const container = document.getElementById(componentName + '-criteria-container');
-  const newCriterion = container.querySelector('.search-criterion').cloneNode(true);
-
-  // Reset values
-  newCriterion.querySelector('.criterion-select').value = '';
-  newCriterion.querySelector('.operator-select').innerHTML = '<option value="">Select operator...</option>';
-  newCriterion.querySelector('.value-input').value = '';
-  newCriterion.querySelector('.value-input').placeholder = 'Enter value...';
-
-  // Remove any state select
-  const stateSelect = newCriterion.querySelector('.state-select');
-  if (stateSelect) {
-    stateSelect.remove();
-  }
-
-  container.appendChild(newCriterion);
-  updateRemoveButtonsVisibility(container);
-}
-
-// Update visibility of remove buttons based on criteria count
-function updateRemoveButtonsVisibility(container) {
-  const criteria = container.querySelectorAll('.search-criterion');
-  const removeButtons = container.querySelectorAll('.remove-criterion');
-
-  removeButtons.forEach(button => {
-    if (criteria.length <= 1) {
-      button.style.display = 'none';
-    } else {
-      button.style.display = 'block';
-    }
-  });
-}
-
-// Remove search criterion
-function removeCriterion(button) {
-  const container = button.closest('[id$="-criteria-container"]');
-  const criteria = container.querySelectorAll('.search-criterion');
-
-  // Don't remove if it's the last criterion
-  if (criteria.length > 1) {
-    button.closest('.search-criterion').remove();
-    updateRemoveButtonsVisibility(container);
-  }
-}
-
-// Build query string from criteria
-function buildQuery(componentName) {
-  const container = document.getElementById(componentName + '-criteria-container');
-  const criteria = container.querySelectorAll('.search-criterion');
-  const queryParts = [];
-
-  criteria.forEach(criterion => {
-    const field = criterion.querySelector('.criterion-select').value;
-    const operator = criterion.querySelector('.operator-select').value;
-    let value = criterion.querySelector('.value-input').value;
-
-    // Check for state select
-    const stateSelect = criterion.querySelector('.state-select');
-    if (stateSelect && stateSelect.style.display !== 'none') {
-      value = stateSelect.value;
-    }
-
-    if (field && operator && value) {
-      queryParts.push(`${field} ${operator} ${value}`);
-    }
-  });
-
-  return queryParts.join('\n');
-}
-
-// Parse existing query and populate dropdowns
-function parseQuery(componentName, query) {
-  if (!query) return;
-
-  const container = document.getElementById(componentName + '-criteria-container');
-  const existingCriteria = container.querySelectorAll('.search-criterion');
-
-  // Remove extra criteria, keeping only the first one
-  for (let i = existingCriteria.length - 1; i > 0; i--) {
-    existingCriteria[i].remove();
-  }
-
-  const lines = query.split('\n').filter(line => line.trim());
-
-  lines.forEach((line, index) => {
-    let criterion;
-
-    if (index === 0) {
-      // Use the existing first criterion
-      criterion = container.querySelector('.search-criterion');
-    } else {
-      // Add additional criteria
-      addCriterion(componentName);
-      const criteria = container.querySelectorAll('.search-criterion');
-      criterion = criteria[criteria.length - 1];
-    }
-
-    // Parse line and populate the criterion
-    const parts = line.trim().match(/^(\w+)\s*(=~|!~|<=|>=|!=|==|=|<|>)\s*(.+)$/);
-
-    if (parts && criterion) {
-      const [, field, operator, value] = parts;
-
-      criterion.querySelector('.criterion-select').value = field;
-      updateOperators(criterion.querySelector('.criterion-select'));
-      criterion.querySelector('.operator-select').value = operator;
-
-      if (field === 'state') {
-        const stateSelect = criterion.querySelector('.state-select');
-        if (stateSelect) {
-          stateSelect.value = value;
-        }
-      } else {
-        criterion.querySelector('.value-input').value = value;
-      }
-    }
-  });
-
-  updateRemoveButtonsVisibility(container);
-}
-
-// Toggle between dropdown and textbox input modes
-function toggleInputMode(componentName) {
-  const dropdownContainer = document.getElementById(componentName + '-criteria-container');
-  const textboxContainer = document.getElementById(componentName + '-textbox-container');
-  const toggleButton = document.getElementById(componentName + '-toggle-mode');
-  const addButton = document.getElementById(componentName + '-add-criterion');
-  const textbox = document.getElementById(componentName + '-input-box');
-  const hiddenInput = document.getElementById(componentName + '-query');
-
-  if (currentMode === 'dropdown') {
-    // Switch to textbox mode and sync dropdown to textbox
-    const query = buildQuery(componentName);
-    textbox.value = query;
-    hiddenInput.value = query;
-
-    dropdownContainer.style.display = 'none';
-    textboxContainer.style.display = 'block';
-    toggleButton.textContent = 'Switch to drop-down query input';
-    addButton.style.display = 'none';
-
-    currentMode = 'textbox';
-  } else {
-    // Switch to dropdown mode and sync textbox to dropdown
-    const query = textbox.value.trim();
-    hiddenInput.value = query;
-
-    dropdownContainer.style.display = 'block';
-    textboxContainer.style.display = 'none';
-    toggleButton.textContent = 'Switch to textbox query input';
-    addButton.style.display = 'block';
-
-    // Parse the textbox query back into dropdowns
-    if (query) {
-      parseQuery(componentName, query);
-    } else {
-      // If textbox is empty, reset to single empty criterion
-      const container = document.getElementById(componentName + '-criteria-container');
-      const criteria = container.querySelectorAll('.search-criterion');
-      // Remove extra criteria, keep only first one
-      for (let i = criteria.length - 1; i > 0; i--) {
-        criteria[i].remove();
-      }
-      // Reset first criterion
-      const firstCriterion = container.querySelector('.search-criterion');
-      if (firstCriterion) {
-        firstCriterion.querySelector('.criterion-select').value = '';
-        firstCriterion.querySelector('.operator-select').innerHTML = '<option value="">Select operator...</option>';
-        firstCriterion.querySelector('.value-input').value = '';
-        const stateSelect = firstCriterion.querySelector('.state-select');
-        if (stateSelect) stateSelect.remove();
-      }
-      updateRemoveButtonsVisibility(container);
-    }
-
-    currentMode = 'dropdown';
-  }
-
-  // Add real-time sync for textbox changes
-  if (currentMode === 'textbox') {
-    // Remove previous listener if any, then add
-    textbox.removeEventListener('input', syncTextboxToHiddenInput);
-    textbox.addEventListener('input', syncTextboxToHiddenInput);
-  }
-}
-// Handler for syncing textbox to hidden input
-function syncTextboxToHiddenInput() {
-  const hiddenInput = document.getElementById("{{ component_name }}-query");
-  const textbox = document.getElementById("{{ component_name }}-input-box");
-  hiddenInput.value = textbox.value;
-}
-
-// Form submission handler
-document.getElementById("{{ component_name }}-form").addEventListener('submit', function(e) {
-  let query;
-  if (currentMode === 'dropdown') {
-    query = buildQuery("{{ component_name }}");
-  } else {
-    query = document.getElementById("{{ component_name }}-input-box").value;
-  }
-  document.getElementById("{{ component_name }}-query").value = query;
-});
-
-// Initialize on page load
-document.addEventListener('DOMContentLoaded', function() {
-  // Initialize search context
-  isJobSearch = document.getElementById("{{ component_name }}-form").getAttribute('data-is-job-search') === 'true';
-
-  const container = document.getElementById("{{ component_name }}-criteria-container");
-  const existingQuery = document.getElementById("{{ component_name }}-query").value;
-  if (existingQuery) {
-    parseQuery("{{ component_name }}", existingQuery);
-  } else {
-    // Update remove button visibility on initial load
-    updateRemoveButtonsVisibility(container);
-  }
-});
-
-// Keyboard shortcut support
-document.addEventListener("keydown", function (e) {
-  if (e.key === "Enter" && (e.metaKey || e.ctrlKey)) {
-    e.preventDefault();
-    let query;
-    if (currentMode === 'dropdown') {
-      query = buildQuery("{{ component_name }}");
-    } else {
-      query = document.getElementById("{{ component_name }}-input-box").value;
-    }
-    document.getElementById("{{ component_name }}-query").value = query;
-    document.getElementById("{{ component_name }}-form").submit();
-  }
-});
-</script>
+<script defer src='{{ base_path }}/batch/static/js/table_search.js'></script>
 {% endmacro %}
diff --git a/batch/batch/utils.py b/batch/batch/utils.py
index 657d6ccd464..351a55d6bd4 100644
--- a/batch/batch/utils.py
+++ b/batch/batch/utils.py
@@ -47,6 +47,33 @@ async def wrapped(request, *args, **kwargs):
     return wrapped
 
 
+def rewrite_dockerhub_image(image: str, dockerhub_prefix: str) -> Optional[str]:
+    """
+    Rewrite a Docker Hub image reference to use a GAR Remote Repository proxy.
+
+    Only rewrites if there's no explicit registry. A registry is indicated by:
+    - Multiple parts separated by '/' where the first part contains '.' or ':'
+    - If there's only one part (no '/'), it's definitely not a registry
+    Returns the rewritten image if it was rewritten, None otherwise.
+    """
+    # Split by '/' to check if there are multiple parts
+    parts = image.split('/', 1)
+
+    # If there's only one part (no '/'), it is a bare image - prepend /library/ and the prefix
+    if len(parts) == 1:
+        return f'{dockerhub_prefix}/library/{image}'
+
+    # Multiple parts - check if the first part looks like a registry
+    first_part = parts[0]
+
+    # If the first part contains '.' or ':', it's a registry domain
+    if '.' in first_part or ':' in first_part:
+        return None
+
+    # No explicit registry, so prepend the dockerhub prefix
+    return f'{dockerhub_prefix}/{image}'
+
+
 def coalesce(x, default):
     if x is not None:
         return x
diff --git a/batch/batch/worker/worker.py b/batch/batch/worker/worker.py
index c6f6824329b..9b922cb563e 100644
--- a/batch/batch/worker/worker.py
+++ b/batch/batch/worker/worker.py
@@ -543,7 +543,10 @@ async def pull():
                 if e.status == 404 and 'pull access denied' in e.message:
                     raise ImageCannotBePulled from e
                 if e.status == 500 and (
-                    ('artifactregistry.repositories.downloadArtifacts' in e.message and 'denied on resource' in e.message)
+                    (
+                        'artifactregistry.repositories.downloadArtifacts' in e.message
+                        and 'denied on resource' in e.message
+                    )
                     or 'Caller does not have permission' in e.message
                     or 'unauthorized' in e.message
                 ):
diff --git a/batch/deployment.yaml b/batch/deployment.yaml
index f392b0e791d..a308ca8af53 100644
--- a/batch/deployment.yaml
+++ b/batch/deployment.yaml
@@ -195,6 +195,12 @@ spec:
              secretKeyRef:
                name: global-config
                key: docker_prefix
+         - name: HAIL_DOCKERHUB_PREFIX
+           valueFrom:
+             secretKeyRef:
+               name: global-config
+               key: dockerhub_prefix
+               optional: true
          - name: KUBERNETES_SERVER_URL
            valueFrom:
              secretKeyRef:
@@ -385,6 +391,12 @@ spec:
              secretKeyRef:
                name: global-config
                key: docker_prefix
+         - name: HAIL_DOCKERHUB_PREFIX
+           valueFrom:
+             secretKeyRef:
+               name: global-config
+               key: dockerhub_prefix
+               optional: true
          - name: KUBERNETES_SERVER_URL
            valueFrom:
              secretKeyRef:
diff --git a/batch/pinned-requirements.txt b/batch/pinned-requirements.txt
index 2a15a2da9b6..685c6b07423 100644
--- a/batch/pinned-requirements.txt
+++ b/batch/pinned-requirements.txt
@@ -1,6 +1,6 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile --python-version 3.10 --python-platform linux batch/requirements.txt --output-file=batch/pinned-requirements.txt
-aiodocker==0.24.0
+aiodocker==0.26.0
     # via -r batch/requirements.txt
 aiohappyeyeballs==2.6.1
     # via
@@ -9,7 +9,7 @@ aiohappyeyeballs==2.6.1
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -c batch/../web_common/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -57,7 +57,7 @@ idna==3.11
     #   -c batch/../hail/python/pinned-requirements.txt
     #   -c batch/../web_common/pinned-requirements.txt
     #   yarl
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -70,7 +70,7 @@ numpy==2.2.6
     #   -c batch/../hail/python/dev/pinned-requirements.txt
     #   -c batch/../hail/python/pinned-requirements.txt
     #   pandas
-packaging==25.0
+packaging==26.0
     # via
     #   -c batch/../gear/pinned-requirements.txt
     #   -c batch/../hail/python/dev/pinned-requirements.txt
@@ -108,7 +108,7 @@ six==1.17.0
     #   -c batch/../hail/python/dev/pinned-requirements.txt
     #   -c batch/../hail/python/pinned-requirements.txt
     #   python-dateutil
-tenacity==9.1.2
+tenacity==9.1.4
     # via
     #   -c batch/../hail/python/pinned-requirements.txt
     #   plotly
@@ -120,7 +120,7 @@ typing-extensions==4.15.0
     #   -c batch/../web_common/pinned-requirements.txt
     #   aiosignal
     #   multidict
-tzdata==2025.2
+tzdata==2025.3
     # via
     #   -c batch/../hail/python/dev/pinned-requirements.txt
     #   -c batch/../hail/python/pinned-requirements.txt
diff --git a/batch/sql/120-add-dockerhub-proxy-flag.sql b/batch/sql/120-add-dockerhub-proxy-flag.sql
new file mode 100644
index 00000000000..1049bab4d34
--- /dev/null
+++ b/batch/sql/120-add-dockerhub-proxy-flag.sql
@@ -0,0 +1 @@
+ALTER TABLE `feature_flags` ADD COLUMN `dockerhub_proxy` BOOLEAN NOT NULL DEFAULT FALSE;
diff --git a/batch/test/test_utils.py b/batch/test/test_utils.py
index d24161cc68e..92947cc5462 100644
--- a/batch/test/test_utils.py
+++ b/batch/test/test_utils.py
@@ -5,6 +5,7 @@
 from batch.cloud.gcp.resource_utils import gcp_worker_memory_per_core_mib, machine_type_to_gpu_num
 from batch.cloud.gcp.resources import GCPAcceleratorResource, gcp_resource_from_dict
 from batch.cloud.resource_utils import adjust_cores_for_packability
+from batch.utils import rewrite_dockerhub_image
 from hailtop.batch_client.parse import parse_memory_in_bytes
 
 
@@ -117,3 +118,39 @@ def test_gcp_accelerator_to_from_dict():
     assert version_2_resource
     version_2_remade_dict = version_2_resource.to_dict()
     assert version_2_remade_dict == version_2_dict
+
+
+@pytest.mark.parametrize(
+    "image,expected",
+    [
+        # Bare images (should be rewritten)
+        ("ubuntu:20.04", "us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/ubuntu:20.04"),
+        ("ubuntu", "us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/ubuntu"),
+        ("python:3.9", "us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/python:3.9"),
+        # Namespaced images (should be rewritten)
+        ("myorg/myimage:tag", "us-central1-docker.pkg.dev/my-project/dockerhubproxy/myorg/myimage:tag"),
+        ("envoyproxy/envoy:v1.33.0", "us-central1-docker.pkg.dev/my-project/dockerhubproxy/envoyproxy/envoy:v1.33.0"),
+        # Images with explicit registry (should NOT be rewritten)
+        ("gcr.io/myproject/image:tag", None),
+        ("us-central1-docker.pkg.dev/project/repo/image", None),
+        ("myregistry.io/image:tag", None),
+        ("localhost:5000/image", None),
+        ("registry.example.com:8080/image", None),
+        # Edge cases
+        (
+            "image.with.dots:tag",
+            "us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/image.with.dots:tag",
+        ),  # dots in first part
+        (
+            "image:with:colons",
+            "us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/image:with:colons",
+        ),  # colons in first part
+        (
+            "my-org/my-image:1.0.0",
+            "us-central1-docker.pkg.dev/my-project/dockerhubproxy/my-org/my-image:1.0.0",
+        ),  # hyphens OK
+    ],
+)
+def test_rewrite_dockerhub_image(image, expected):
+    dockerhub_prefix = "us-central1-docker.pkg.dev/my-project/dockerhubproxy"
+    assert rewrite_dockerhub_image(image, dockerhub_prefix) == expected
diff --git a/build.yaml b/build.yaml
index 5df8460138a..7ae3c416cf8 100644
--- a/build.yaml
+++ b/build.yaml
@@ -1,4228 +1,4040 @@
 steps:
-  - kind: buildImage2
-    name: git_make_bash_image
-    publishAs: git-make-bash
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ global.docker_root_image }}
-        FROM $BASE_IMAGE
-        RUN apt-get update && apt-get install -y git make bash
-  - kind: runImage
-    name: merge_code
-    image:
-      valueFrom: git_make_bash_image.image
-    script: |
-      set -ex
-      cd /io
-      mkdir -p repo
-      cd repo
-      {{ code.checkout_script }}
-      make -C hail python-version-info HAIL_BUILD_MODE=Release MILLOPTS=--no-daemon
-    outputs:
-      - from: /io/repo/
-        to: /repo
-    dependsOn:
-      - git_make_bash_image
-  - kind: createNamespace
-    name: default_ns
-    namespaceName: default
-    secrets:
-      - name: auth-oauth2-client-secret
-      - name: hail-ci-0-1-github-oauth-token
-      - name: testns-test-gsa-key
-      - name: testns-test-dev-gsa-key
-      - name: testns-auth-gsa-key
-      - name: testns-batch-gsa-key
-      - name: testns-ci-gsa-key
-      - name: testns-grafana-gsa-key
-      - name: test-aws-key
-        clouds:
-          - gcp
-      - name: test-azure-key
-        clouds:
-          - gcp
-      - name: zulip-config
-      - name: billing-monitor-gsa-key
-        clouds:
-          - gcp
-      - name: hail-ci-0-1-service-account-key
-      - name: batch-worker-ssh-public-key
-        clouds:
-          - azure
-  - kind: runImage
-    name: copy_third_party_images
-    image: quay.io/skopeo/stable:v1.13.2
-    script: |
-      set -ex
-
-      retry() {
-          "$@" ||
-              (sleep 2 && "$@") ||
-              (sleep 5 && "$@");
-      }
-
-      REGISTRY={{ global.docker_prefix.split('/')[0] }}
-
-      {% if global.cloud == "gcp" %}
-      cat $GOOGLE_APPLICATION_CREDENTIALS | base64 -w 0 | skopeo login -u _json_key_base64 --password-stdin $REGISTRY
-      {% elif global.cloud == "azure" %}
-      dnf install -y jq
-      USERNAME=$(cat $AZURE_APPLICATION_CREDENTIALS | jq -jr '.appId')
-      cat $AZURE_APPLICATION_CREDENTIALS | jq -jr '.password' | skopeo login -u $USERNAME --password-stdin $REGISTRY
-      {% else %}
-      echo "unknown cloud {{ global.cloud }}"
-      exit 1
-      {% endif %}
-
-      cd /io/docker/third-party
-      DOCKER_PREFIX={{ global.docker_prefix }} retry bash copy_images.sh
-    inputs:
-      - from: /repo/docker
-        to: /io/docker
-    scopes:
-      - deploy
-    dependsOn:
-      - default_ns
-      - merge_code
-  - kind: buildImage2
-    name: hail_ubuntu_image
-    dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
-    contextPath: /io/repo
-    publishAs: hail-ubuntu
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/docker/hail-ubuntu
-        to: /io/repo/docker/hail-ubuntu
-      - from: /repo/gear/pinned-requirements.txt
-        to: /io/repo/gear/pinned-requirements.txt
-    dependsOn:
-      - merge_code
-      - copy_third_party_images
-  - kind: buildImage2
-    name: hail_ubuntu_image_python_3_10
-    dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
-    contextPath: /io/repo
-    publishAs: hail-ubuntu-python-3-10
-    buildArgs:
-      - name: PYTHON_VERSION
-        value: "3.10"
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/docker/hail-ubuntu
-        to: /io/repo/docker/hail-ubuntu
-      - from: /repo/gear/pinned-requirements.txt
-        to: /io/repo/gear/pinned-requirements.txt
-    dependsOn:
-      - merge_code
-      - copy_third_party_images
-  - kind: buildImage2
-    name: hail_ubuntu_image_python_3_12
-    dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
-    contextPath: /io/repo
-    publishAs: hail-ubuntu-python-3-12
-    buildArgs:
-      - name: PYTHON_VERSION
-        value: "3.12"
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/docker/hail-ubuntu
-        to: /io/repo/docker/hail-ubuntu
-      - from: /repo/gear/pinned-requirements.txt
-        to: /io/repo/gear/pinned-requirements.txt
-    dependsOn:
-      - merge_code
-      - copy_third_party_images
-  - kind: buildImage2
-    name: hail_ubuntu_image_python_3_13
-    dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
-    contextPath: /io/repo
-    publishAs: hail-ubuntu-python-3-13
-    buildArgs:
-      - name: PYTHON_VERSION
-        value: "3.13"
-      - name: SKIP_GCLOUD_PROFILER
-        value: "true" # Python 3.13 does not support google-cloud-profiler yet
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/docker/hail-ubuntu
-        to: /io/repo/docker/hail-ubuntu
-      - from: /repo/gear/pinned-requirements.txt
-        to: /io/repo/gear/pinned-requirements.txt
-    dependsOn:
-      - merge_code
-      - copy_third_party_images
-  - kind: deploy
-    name: deploy_batch_sa
+- kind: buildImage2
+  name: git_make_bash_image
+  publishAs: git-make-bash
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ global.docker_root_image }}
+      FROM $BASE_IMAGE
+      RUN apt-get update && apt-get install -y git make bash
+- kind: runImage
+  name: merge_code
+  image:
+    valueFrom: git_make_bash_image.image
+  script: |
+    set -ex
+    cd /io
+    mkdir -p repo
+    cd repo
+    {{ code.checkout_script }}
+    make -C hail python-version-info HAIL_BUILD_MODE=Release MILLOPTS=--no-daemon
+  outputs:
+  - from: /io/repo/
+    to: /repo
+  dependsOn:
+  - git_make_bash_image
+- kind: createNamespace
+  name: default_ns
+  namespaceName: default
+  secrets:
+  - name: auth-oauth2-client-secret
+  - name: hail-ci-0-1-github-oauth-token
+  - name: testns-test-gsa-key
+  - name: testns-test-dev-gsa-key
+  - name: testns-auth-gsa-key
+  - name: testns-batch-gsa-key
+  - name: testns-ci-gsa-key
+  - name: testns-grafana-gsa-key
+  - name: test-aws-key
+    clouds:
+    - gcp
+  - name: test-azure-key
+    clouds:
+    - gcp
+  - name: zulip-config
+  - name: billing-monitor-gsa-key
+    clouds:
+    - gcp
+  - name: hail-ci-0-1-service-account-key
+- kind: runImage
+  name: copy_third_party_images
+  image: quay.io/skopeo/stable:v1.13.2
+  script: |
+    set -ex
+
+    retry() {
+        "$@" ||
+            (sleep 2 && "$@") ||
+            (sleep 5 && "$@");
+    }
+
+    REGISTRY={{ global.docker_prefix.split('/')[0] }}
+
+    {% if global.cloud == "gcp" %}
+    cat $GOOGLE_APPLICATION_CREDENTIALS | base64 -w 0 | skopeo login -u _json_key_base64 --password-stdin $REGISTRY
+    {% else %}
+    echo "unknown cloud {{ global.cloud }}"
+    exit 1
+    {% endif %}
+
+    cd /io/docker/third-party
+    DOCKER_PREFIX={{ global.docker_prefix }} {% if global.dockerhub_prefix %}DOCKERHUB_PREFIX={{ global.dockerhub_prefix }} {% endif %}retry bash copy_images.sh
+  inputs:
+  - from: /repo/docker
+    to: /io/docker
+  scopes:
+  - deploy
+  dependsOn:
+  - default_ns
+  - merge_code
+- kind: buildImage2
+  name: hail_ubuntu_image
+  dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
+  contextPath: /io/repo
+  publishAs: hail-ubuntu
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/docker/hail-ubuntu
+    to: /io/repo/docker/hail-ubuntu
+  - from: /repo/gear/pinned-requirements.txt
+    to: /io/repo/gear/pinned-requirements.txt
+  dependsOn:
+  - merge_code
+  - copy_third_party_images
+- kind: buildImage2
+  name: hail_ubuntu_image_python_3_10
+  dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
+  contextPath: /io/repo
+  publishAs: hail-ubuntu-python-3-10
+  buildArgs:
+  - name: PYTHON_VERSION
+    value: "3.10"
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/docker/hail-ubuntu
+    to: /io/repo/docker/hail-ubuntu
+  - from: /repo/gear/pinned-requirements.txt
+    to: /io/repo/gear/pinned-requirements.txt
+  dependsOn:
+  - merge_code
+  - copy_third_party_images
+- kind: buildImage2
+  name: hail_ubuntu_image_python_3_12
+  dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
+  contextPath: /io/repo
+  publishAs: hail-ubuntu-python-3-12
+  buildArgs:
+  - name: PYTHON_VERSION
+    value: "3.12"
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/docker/hail-ubuntu
+    to: /io/repo/docker/hail-ubuntu
+  - from: /repo/gear/pinned-requirements.txt
+    to: /io/repo/gear/pinned-requirements.txt
+  dependsOn:
+  - merge_code
+  - copy_third_party_images
+- kind: buildImage2
+  name: hail_ubuntu_image_python_3_13
+  dockerFile: /io/repo/docker/hail-ubuntu/Dockerfile
+  contextPath: /io/repo
+  publishAs: hail-ubuntu-python-3-13
+  buildArgs:
+  - name: PYTHON_VERSION
+    value: "3.13"
+  - name: SKIP_GCLOUD_PROFILER
+    value: "true" # Python 3.13 does not support google-cloud-profiler yet
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/docker/hail-ubuntu
+    to: /io/repo/docker/hail-ubuntu
+  - from: /repo/gear/pinned-requirements.txt
+    to: /io/repo/gear/pinned-requirements.txt
+  dependsOn:
+  - merge_code
+  - copy_third_party_images
+- kind: deploy
+  name: deploy_batch_sa
+  namespace:
+    valueFrom: default_ns.name
+  config: batch/service-account.yaml
+  dependsOn:
+  - default_ns
+- kind: deploy
+  name: deploy_ci_agent
+  namespace:
+    valueFrom: default_ns.name
+  config: ci/ci-agent.yaml
+  dependsOn:
+  - default_ns
+- kind: deploy
+  name: deploy_test_batch_sa
+  namespace:
+    valueFrom: default_ns.name
+  config: batch/test-sa.yaml
+  dependsOn:
+  - default_ns
+- kind: buildImage2
+  name: base_image
+  dockerFile: /io/repo/docker/Dockerfile.base
+  contextPath: /io/repo
+  publishAs: base
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/docker/Dockerfile.base
+    to: /io/repo/docker/Dockerfile.base
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: buildImage2
+  name: create_certs_image
+  dockerFile: /io/tls/Dockerfile
+  contextPath: /io/tls
+  publishAs: create_certs_image
+  inputs:
+  - from: /repo/tls
+    to: /io/tls
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: runImage
+  name: create_ssl_config_hail_root
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: create_certs_image.image
+  script: |
+    
+    {% if not deploy %}
+    kubectl get secret -n {{ default_ns.name }} ssl-config-hail-root \
+      --template={% raw %}'{{index .data "hail-root-cert.pem"}}'{% endraw %} \
+      | base64 --decode \
+      | openssl x509 -checkend 0 -noout -in -
+
+    if [ "$?" -ne 0 ]
+    then
+        kubectl delete secret -n {{ default_ns.name }} ssl-config-hail-root
+    fi
+    {% endif %}
+
+    openssl req -new -x509 -subj /CN=hail-root -nodes -newkey rsa:4096 -keyout hail-root-key.pem -out hail-root-cert.pem
+    until kubectl get secret -n {{ default_ns.name }} ssl-config-hail-root
+    do
+        kubectl create secret generic -n {{ default_ns.name }} ssl-config-hail-root \
+                --from-file=hail-root-key.pem \
+                --from-file=hail-root-cert.pem
+    done
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: batch/service-account.yaml
-    dependsOn:
-      - default_ns
-  - kind: deploy
-    name: deploy_ci_agent
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - default_ns
+  - create_certs_image
+- kind: runImage
+  name: create_certs
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: create_certs_image.image
+  script: |
+    set -ex
+    python3 create_certs.py \
+            {{ default_ns.name }} \
+            config.yaml \
+            /ssl-config-hail-root/hail-root-key.pem \
+            /ssl-config-hail-root/hail-root-cert.pem
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: ci/ci-agent.yaml
-    dependsOn:
-      - default_ns
-  - kind: deploy
-    name: deploy_test_batch_sa
+  secrets:
+  - name: ssl-config-hail-root
     namespace:
       valueFrom: default_ns.name
-    config: batch/test-sa.yaml
-    dependsOn:
-      - default_ns
-  - kind: buildImage2
-    name: base_image
-    dockerFile: /io/repo/docker/Dockerfile.base
-    contextPath: /io/repo
-    publishAs: base
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/docker/Dockerfile.base
-        to: /io/repo/docker/Dockerfile.base
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: buildImage2
-    name: create_certs_image
-    dockerFile: /io/tls/Dockerfile
-    contextPath: /io/tls
-    publishAs: create_certs_image
-    inputs:
-      - from: /repo/tls
-        to: /io/tls
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: runImage
-    name: create_ssl_config_hail_root
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: create_certs_image.image
-    script: |
-
-      {% if not deploy %}
-      kubectl get secret -n {{ default_ns.name }} ssl-config-hail-root \
-        --template={% raw %}'{{index .data "hail-root-cert.pem"}}'{% endraw %} \
-        | base64 --decode \
-        | openssl x509 -checkend 0 -noout -in -
-
-      if [ "$?" -ne 0 ]
-      then
-          kubectl delete secret -n {{ default_ns.name }} ssl-config-hail-root
-      fi
-      {% endif %}
-
-      openssl req -new -x509 -subj /CN=hail-root -nodes -newkey rsa:4096 -keyout hail-root-key.pem -out hail-root-cert.pem
-      until kubectl get secret -n {{ default_ns.name }} ssl-config-hail-root
-      do
-          kubectl create secret generic -n {{ default_ns.name }} ssl-config-hail-root \
-                  --from-file=hail-root-key.pem \
-                  --from-file=hail-root-cert.pem
-      done
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - default_ns
-      - create_certs_image
-  - kind: runImage
-    name: create_certs
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: create_certs_image.image
-    script: |
-      set -ex
-      python3 create_certs.py \
-              {{ default_ns.name }} \
-              config.yaml \
-              /ssl-config-hail-root/hail-root-key.pem \
-              /ssl-config-hail-root/hail-root-cert.pem
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    secrets:
-      - name: ssl-config-hail-root
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /ssl-config-hail-root
-    dependsOn:
-      - default_ns
-      - create_certs_image
-      - create_ssl_config_hail_root
-  - kind: buildImage2
-    name: ci_utils_image
-    dockerFile: /io/repo/ci/Dockerfile.ci-utils
-    contextPath: /io/repo
-    publishAs: ci-utils
-    resources:
-      storage: 20Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/ci
-        to: /io/repo/ci
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: create_test_database_server_config
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: create_certs_image.image
-    script: |
-      # Check if secret exists and get its age
-      # First, set +ex to (e) allow the command to fail, (x) avoid logging the password
-      set +ex
-      echo 'Running: SECRET_JSON=$(kubectl get secret database-server-config -n {{ default_ns.name }} -o json --show-managed-fields)'
-      SECRET_JSON=$(kubectl get secret database-server-config -n {{ default_ns.name }} -o json --show-managed-fields)
-      SECRET_EXISTS_EXIT_CODE=$?
-      echo "SECRET_EXISTS_EXIT_CODE=$SECRET_EXISTS_EXIT_CODE"
-      set -ex
-
-      if [ "$SECRET_EXISTS_EXIT_CODE" -eq 0 ]; then
-          echo "Secret exists, checking age..."
-
-          # Extract the latest timestamp from managed fields
-          set +x
-          echo "Running: LATEST_TIME=\$(echo \"\$SECRET_JSON\" | jq -r '.metadata.managedFields[] | .time' | sort -r | head -n1)"
-          LATEST_TIME=$(echo "$SECRET_JSON" | jq -r '.metadata.managedFields[] | .time' | sort -r | head -n1)
-          set -x
-          
-          echo "Latest secret modification time: $LATEST_TIME"
-          
-          # Convert to timestamp and check if over 1 year old (365 days)
-          TIMESTAMP=$(date -d "$LATEST_TIME" +%s 2>/dev/null || echo "0")
-          CURRENT_TIME=$(date +%s)
-          AGE_DAYS=$(( (CURRENT_TIME - TIMESTAMP) / 86400 ))
-          
-          echo "Secret age: $AGE_DAYS days"
-          
-          if [ "$AGE_DAYS" -gt 365 ]; then
-              echo "Secret is over 1 year old, regenerating certificates while preserving password..."
-              
-              # Turn off set -x to avoid logging password:
-              set +x
-              echo "Running: EXISTING_PASSWORD=\$(echo \"\$SECRET_JSON\" | jq -r '.data[\"db-root-password\"]' | base64 -d)"
-              EXISTING_PASSWORD=$(echo "$SECRET_JSON" | jq -r '.data["db-root-password"]' | base64 -d)
-              # Regenerate certificates with existing password (disable set -x to avoid logging password)
-              echo "Running: NAMESPACE={{ default_ns.name }} KEEP_PASSWORD=\"\$EXISTING_PASSWORD\" bash /create_test_db_config.sh"
-              NAMESPACE={{ default_ns.name }} KEEP_PASSWORD="$EXISTING_PASSWORD" bash /create_test_db_config.sh
-              set -x
-          else
-              echo "Secret is less than 1 year old, skipping regeneration"
-          fi
-      else
-          echo "Secret does not exist, creating new one..."
-          NAMESPACE={{ default_ns.name }} bash /create_test_db_config.sh
-      fi
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    scopes:
-      - dev
-      - test
-    dependsOn:
-      - default_ns
-      - create_certs_image
-  - kind: deploy
-    name: deploy_test_db
+    mountPath: /ssl-config-hail-root
+  dependsOn:
+  - default_ns
+  - create_certs_image
+  - create_ssl_config_hail_root
+- kind: buildImage2
+  name: ci_utils_image
+  dockerFile: /io/repo/ci/Dockerfile.ci-utils
+  contextPath: /io/repo
+  publishAs: ci-utils
+  resources:
+    storage: 20Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/ci
+    to: /io/repo/ci
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: runImage
+  name: create_test_database_server_config
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: create_certs_image.image
+  script: |
+    # Check if secret exists and get its age
+    # First, set +ex to (e) allow the command to fail, (x) avoid logging the password
+    set +ex
+    echo 'Running: SECRET_JSON=$(kubectl get secret database-server-config -n {{ default_ns.name }} -o json --show-managed-fields)'
+    SECRET_JSON=$(kubectl get secret database-server-config -n {{ default_ns.name }} -o json --show-managed-fields)
+    SECRET_EXISTS_EXIT_CODE=$?
+    echo "SECRET_EXISTS_EXIT_CODE=$SECRET_EXISTS_EXIT_CODE"
+    set -ex
+
+    if [ "$SECRET_EXISTS_EXIT_CODE" -eq 0 ]; then
+        echo "Secret exists, checking age..."
+
+        # Extract the latest timestamp from managed fields
+        set +x
+        echo "Running: LATEST_TIME=\$(echo \"\$SECRET_JSON\" | jq -r '.metadata.managedFields[] | .time' | sort -r | head -n1)"
+        LATEST_TIME=$(echo "$SECRET_JSON" | jq -r '.metadata.managedFields[] | .time' | sort -r | head -n1)
+        set -x
+        
+        echo "Latest secret modification time: $LATEST_TIME"
+        
+        # Convert to timestamp and check if over 1 year old (365 days)
+        TIMESTAMP=$(date -d "$LATEST_TIME" +%s 2>/dev/null || echo "0")
+        CURRENT_TIME=$(date +%s)
+        AGE_DAYS=$(( (CURRENT_TIME - TIMESTAMP) / 86400 ))
+        
+        echo "Secret age: $AGE_DAYS days"
+        
+        if [ "$AGE_DAYS" -gt 365 ]; then
+            echo "Secret is over 1 year old, regenerating certificates while preserving password..."
+            
+            # Turn off set -x to avoid logging password:
+            set +x
+            echo "Running: EXISTING_PASSWORD=\$(echo \"\$SECRET_JSON\" | jq -r '.data[\"db-root-password\"]' | base64 -d)"
+            EXISTING_PASSWORD=$(echo "$SECRET_JSON" | jq -r '.data["db-root-password"]' | base64 -d)
+            # Regenerate certificates with existing password (disable set -x to avoid logging password)
+            echo "Running: NAMESPACE={{ default_ns.name }} KEEP_PASSWORD=\"\$EXISTING_PASSWORD\" bash /create_test_db_config.sh"
+            NAMESPACE={{ default_ns.name }} KEEP_PASSWORD="$EXISTING_PASSWORD" bash /create_test_db_config.sh
+            set -x
+        else
+            echo "Secret is less than 1 year old, skipping regeneration"
+        fi
+    else
+        echo "Secret does not exist, creating new one..."
+        NAMESPACE={{ default_ns.name }} bash /create_test_db_config.sh
+    fi
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: docker/mysql/db.yaml
-    wait:
-      - kind: Service
-        name: db
-        for: alive
-        resource_type: statefulset
-    scopes:
-      - dev
-      - test
-    dependsOn:
-      - default_ns
-      - create_test_database_server_config
-  - kind: buildImage2
-    name: admin_pod_image
-    dockerFile: /io/repo/admin-pod/Dockerfile
-    contextPath: /io/repo
-    publishAs: admin-pod
-    inputs:
-      - from: /repo/admin-pod
-        to: /io/repo/admin-pod
-    dependsOn:
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: auth_image
-    dockerFile: /io/repo/auth/Dockerfile
-    contextPath: /io/repo
-    publishAs: auth
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/auth
-        to: /io/repo/auth
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: runImage
-    name: delete_auth_tables
-    image:
-      valueFrom: auth_image.image
-    script: |
-      set -ex
-      cd /io
-      python3 delete_dev_database.py {{ default_ns.name }} auth
-    inputs:
-      - from: /repo/ci/delete_dev_database.py
-        to: /io/delete_dev_database.py
-    secrets:
-      - name: database-server-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /sql-config
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    network: private
-    runIfRequested: true
-    scopes:
-      - dev
-    dependsOn:
-      - default_ns
-      - auth_image
-      - merge_code
-      - create_test_database_server_config
-  - kind: createDatabase2
-    name: auth_database
-    databaseName: auth
-    image:
-      valueFrom: ci_utils_image.image
-    migrations:
-      - name: initial
-        script: /io/sql/000-initial.sql
-      - name: copy-paste-tokens
-        script: /io/sql/001-copy-paste-tokens.sql
-      - name: drop-bucket
-        script: /io/sql/002-drop-bucket.sql
-      - name: add-trial-billing-project
-        script: /io/sql/003-add-trial-billing-project.sql
-      - name: add-roles
-        script: /io/sql/004-add-roles.sql
-      - name: rename-gsa-identity
-        script: /io/sql/005-rename-gsa-identity.sql
-      - name: support-azure-oauth
-        script: /io/sql/006-support-azure-oauth.sql
-      - name: change-username-collation
-        script: /io/sql/007-change-username-collation.sql
-      - name: add-hail-identity-uid
-        script: /io/sql/008-add-hail-identity-uid.sql
-      - name: add-users-last-active
-        script: /io/sql/009-add-users-last-active.sql
-      - name: refactor-roles
-        script: /io/sql/010-refactor-roles.sql
-    inputs:
-      - from: /repo/auth/sql
-        to: /io/sql
+  scopes:
+  - dev
+  - test
+  dependsOn:
+  - default_ns
+  - create_certs_image
+- kind: deploy
+  name: deploy_test_db
+  namespace:
+    valueFrom: default_ns.name
+  config: docker/mysql/db.yaml
+  wait:
+  - kind: Service
+    name: db
+    for: alive
+    resource_type: statefulset
+  scopes:
+  - dev
+  - test
+  dependsOn:
+  - default_ns
+  - create_test_database_server_config
+- kind: buildImage2
+  name: admin_pod_image
+  dockerFile: /io/repo/admin-pod/Dockerfile
+  contextPath: /io/repo
+  publishAs: admin-pod
+  inputs:
+  - from: /repo/admin-pod
+    to: /io/repo/admin-pod
+  dependsOn:
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: auth_image
+  dockerFile: /io/repo/auth/Dockerfile
+  contextPath: /io/repo
+  publishAs: auth
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/auth
+    to: /io/repo/auth
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: runImage
+  name: delete_auth_tables
+  image:
+    valueFrom: auth_image.image
+  script: |
+    set -ex
+    cd /io
+    python3 delete_dev_database.py {{ default_ns.name }} auth
+  inputs:
+  - from: /repo/ci/delete_dev_database.py
+    to: /io/delete_dev_database.py
+  secrets:
+  - name: database-server-config
     namespace:
       valueFrom: default_ns.name
-    shutdowns:
-      - kind: Deployment
-        namespace:
-          valueFrom: default_ns.name
-        name: auth
-    dependsOn:
-      - default_ns
-      - merge_code
-      - delete_auth_tables
-      - ci_utils_image
-      - create_test_database_server_config
-      - deploy_test_db
-  - kind: runImage
-    name: create_deploy_config
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-
-      # k8s deploy config
-      {% if default_ns.name == "default" %}
-      cat > deploy-config.json <<EOF
-      {"location":"k8s","default_namespace":"{{ default_ns.name }}","domain":"{{ global.domain }}"}
-      EOF
-      {% else %}
-      cat > deploy-config.json <<EOF
-      {"location":"k8s","default_namespace":"{{ default_ns.name }}","domain":"internal.{{ global.domain }}","base_path":"/{{ default_ns.name }}"}
-      EOF
-      {% endif %}
-      kubectl -n {{ default_ns.name }} create secret generic deploy-config \
-              --from-file=./deploy-config.json \
-              --save-config --dry-run=client -o yaml \
-          | kubectl -n {{ default_ns.name }} apply -f -
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-  - kind: deploy
-    name: deploy_admin_pod
+    mountPath: /sql-config
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: admin-pod/admin-pod.yaml
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - admin_pod_image
-      - create_deploy_config
-      - create_certs
-  - kind: runImage
-    name: create_session_key
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      # create session keys
-      N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers session-secret-key | wc -l | tr -d '[:space:]')
-      if [[ $N != 0 ]]; then
-        exit
-      fi
-      mkdir /session-secret-key
-      cat > generate-session-key.py <<EOF
-      import base64
-      from cryptography import fernet
-      with open('/session-secret-key/session-secret-key', 'wb') as f:
-          f.write(base64.urlsafe_b64decode(fernet.Fernet.generate_key()))
-      EOF
-      python3 generate-session-key.py
-      kubectl -n {{ default_ns.name }} create secret generic session-secret-key --from-file=/session-secret-key/session-secret-key
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-  - kind: runImage
-    name: create_test_gsa_keys
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      kubectl -n {{ default_ns.name }} get -o json secret testns-test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "test-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-      kubectl -n {{ default_ns.name }} get -o json secret testns-test-dev-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "test-dev-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-      kubectl -n {{ default_ns.name }} get -o json secret testns-auth-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "auth-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-      kubectl -n {{ default_ns.name }} get -o json secret testns-batch-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "batch-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-      kubectl -n {{ default_ns.name }} get -o json secret testns-ci-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "ci-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-      kubectl -n {{ default_ns.name }} get -o json secret testns-grafana-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "grafana-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
-    scopes:
-      - test
-      - dev
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-  - kind: deploy
-    name: deploy_auth_driver_service_account
+  network: private
+  runIfRequested: true
+  scopes:
+  - dev
+  dependsOn:
+  - default_ns
+  - auth_image
+  - merge_code
+  - create_test_database_server_config
+- kind: createDatabase2
+  name: auth_database
+  databaseName: auth
+  image:
+    valueFrom: ci_utils_image.image
+  migrations:
+  - name: initial
+    script: /io/sql/000-initial.sql
+  - name: copy-paste-tokens
+    script: /io/sql/001-copy-paste-tokens.sql
+  - name: drop-bucket
+    script: /io/sql/002-drop-bucket.sql
+  - name: add-trial-billing-project
+    script: /io/sql/003-add-trial-billing-project.sql
+  - name: add-roles
+    script: /io/sql/004-add-roles.sql
+  - name: rename-gsa-identity
+    script: /io/sql/005-rename-gsa-identity.sql
+  - name: support-azure-oauth
+    script: /io/sql/006-support-azure-oauth.sql
+  - name: change-username-collation
+    script: /io/sql/007-change-username-collation.sql
+  - name: add-hail-identity-uid
+    script: /io/sql/008-add-hail-identity-uid.sql
+  - name: add-users-last-active
+    script: /io/sql/009-add-users-last-active.sql
+  - name: refactor-roles
+    script: /io/sql/010-refactor-roles.sql
+  inputs:
+  - from: /repo/auth/sql
+    to: /io/sql
+  namespace:
+    valueFrom: default_ns.name
+  shutdowns:
+  - kind: Deployment
     namespace:
       valueFrom: default_ns.name
-    config: auth/auth-driver-service-account.yaml
-    dependsOn:
-      - default_ns
-  - kind: runImage
-    name: create_accounts
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: auth_image.image
-    script: |
-      set -ex
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_SCOPE={{ scope }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/auth-gsa-key/key.json
-
-      python3 /io/bootstrap_create_accounts.py
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    network: private
-    secrets:
-      - name:
-          valueFrom: auth_database.user_secret_name
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /sql-config
-      - name: database-server-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /database-server-config
-      - name: auth-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /auth-gsa-key
-      - name: global-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /global-config
-    inputs:
-      - from: /repo/ci/bootstrap_create_accounts.py
-        to: /io/bootstrap_create_accounts.py
-    dependsOn:
-      - default_ns
-      - deploy_test_batch_sa
-      - auth_database
-      - auth_image
-      - create_deploy_config
-      - deploy_auth_driver_service_account
-      - create_test_gsa_keys
-      - create_test_database_server_config
-  - kind: buildImage2
-    name: hailgenetics_vep_grch37_85_image
-    dockerFile: /io/repo/docker/hailgenetics/vep/grch37/85/Dockerfile
-    contextPath: /io/repo/docker/vep/
-    publishAs: hailgenetics/vep-grch37-85
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - merge_code
-  - kind: buildImage2
-    name: hailgenetics_vep_grch38_95_image
-    dockerFile: /io/repo/docker/hailgenetics/vep/grch38/95/Dockerfile
-    contextPath: /io/repo/docker/vep/
-    publishAs: hailgenetics/vep-grch38-95
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - merge_code
-  - kind: buildImage2
-    name: monitoring_image
-    dockerFile: /io/repo/monitoring/Dockerfile
-    contextPath: /io/repo
-    publishAs: monitoring
-    inputs:
-      - from: /repo/monitoring
-        to: /io/repo/monitoring
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: buildImage2
-    name: batch_image
-    dockerFile: /io/repo/batch/Dockerfile
-    contextPath: /io/repo
-    publishAs: batch
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/batch
-        to: /io/repo/batch
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: buildImage2
-    name: hailgenetics_hailtop_image
-    dockerFile: /io/repo/docker/hailgenetics/hailtop/Dockerfile
-    contextPath: /io/repo
-    publishAs: hailgenetics/hailtop
-    inputs:
-      - from: /repo/docker/hailgenetics/hailtop
-        to: /io/repo/docker/hailgenetics/hailtop
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-    dependsOn:
-      - merge_code
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: ci_image
-    dockerFile: /io/repo/ci/Dockerfile
-    contextPath: /io/repo
-    publishAs: ci
-    inputs:
-      - from: /repo/ci
-        to: /io/repo/ci
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-    dependsOn:
-      - hail_ubuntu_image
-      - merge_code
-  - kind: buildImage2
-    name: hail_buildkit_image
-    dockerFile: /io/repo/ci/buildkit/Dockerfile
-    contextPath: /io/repo/ci
-    publishAs: hail-buildkit
-    inputs:
-      - from: /repo/ci
-        to: /io/repo/ci
-    dependsOn:
-      - merge_code
-      - copy_third_party_images
-  - kind: runImage
-    name: build_hail_jar_and_wheel
-    image:
-      valueFrom: base_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=Release
-      time retry sh mill --no-daemon --version
-
-      # We've encountered the following sporadic error in CI between `mill`
-      # finishing assembling the jar and `Make` copying the jar:
-      #
-      # cp -f out/assembly.dest/out.jar python/hail/backend/hail-all-spark.jar
-      # cp: cannot stat 'out/assembly.dest/out.jar': No such file or directory
-      #
-      # This was likely from running mill in server mode; mill main exits before
-      # the jar has finished being written.
-      time retry make shadowJar
-      if [ ! -f out/hail/2.12/assembly.dest/out.jar ]; then
-          echo 'no out.jar found after mill assembly returned. going to sleep'
-          sleep 5
-      fi
-
-      time retry make DEV_CLARIFIER=hail-ci-build wheel
-
-      # Check wheel size is small enough for pypi (< 200 MiB)
-      BYTES=$(du build/deploy/dist/hail-*-py3-none-any.whl | awk '{print $1}')
-      (( BYTES < 209715200 )) || exit 1
-    inputs:
-      - from: /repo
-        to: /io/repo
-    outputs:
-      - from: /io/repo/hail/out
-        to: /derived/release/hail/out/
-      - from: /io/repo/hail/build/deploy/dist
-        to: /derived/release/hail/build/deploy/dist
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: upload_temporary_hailctl_artifacts
-    image:
-      valueFrom: ci_utils_image.image
-    resources:
-      memory: standard
-      cpu: '1'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
-      make HAIL_BUILD_MODE=Release DEV_CLARIFIER=hail-ci-build upload-artifacts \
-          -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
-    dependsOn:
-      - ci_utils_image
-      - default_ns
-      - merge_code
-      - build_hail_jar_and_wheel
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/hail/build/deploy/dist
-    secrets:
-      - name: test-dataproc-service-account-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dataproc-service-account-key
-    scopes:
-      - deploy
-      - dev
-    clouds:
-      - gcp
-  - kind: runImage
-    name: build_hail_debug_jar_and_wheel
-    image:
-      valueFrom: base_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=CI
-      time retry sh mill --no-daemon --version
-
-      # See `build_hail_jar_and_wheel`
-      time retry make shadowJar
-      if [ ! -f out/hail/2.12/assembly.dest/out.jar ]; then
-          echo 'no out.jar found after mill assembly returned. going to sleep'
-          sleep 5
-      fi
-
-      time retry make wheel
-    inputs:
-      - from: /repo
-        to: /io/repo
-    outputs:
-      - from: /io/repo/hail/out
-        to: /derived/debug/hail/out
-      - from: /io/repo/hail/build/deploy/dist
-        to: /derived/debug/hail/build/deploy/dist
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: build_debug_hail_test_jar
-    image:
-      valueFrom: base_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=CI
-      time retry sh mill --no-daemon --version
-
-      # See `build_hail_jar_and_wheel`
-      time retry make shadowTestJar
-      if [ ! -f out/hail/2.12/test/assembly.dest/out.jar ]; then
-          echo 'no out.jar found after mill assembly returned. going to sleep'
-          sleep 5
-      fi
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/debug/hail/out
-        to: /io/repo/hail/out
-    outputs:
-      - from: /io/repo/hail/out
-        to: /derived/debug/hail/out
-    dependsOn:
-      - base_image
-      - merge_code
-      - build_hail_debug_jar_and_wheel
-  - kind: runImage
-    name: build_hail_test_artifacts
-    image:
-      valueFrom: base_image.image
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      time tar czf test.tar.gz -C python test pytest.ini
-      time tar czf resources.tar.gz -C hail/test resources
-      time tar czf data.tar.gz -C python/hail/docs data
-      time TESTNG_SPLITS=5 python3 generate_splits.py
-      time tar czf splits.tar.gz testng-splits-*.xml
-    inputs:
-      - from: /repo
-        to: /io/repo
-    outputs:
-      - from: /io/repo/hail/test.tar.gz
-        to: /test.tar.gz
-      - from: /io/repo/hail/resources.tar.gz
-        to: /resources.tar.gz
-      - from: /io/repo/hail/splits.tar.gz
-        to: /splits.tar.gz
-      - from: /io/repo/hail/data.tar.gz
-        to: /data.tar.gz
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: build_azure_wheel
-    image:
-      valueFrom: base_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      export SPARK_VERSION="3.0.2" SCALA_VERSION="2.12.13" HAIL_BUILD_MODE=Release MILLOPTS='--no-daemon'
-      time retry sh mill --no-daemon --version
-
-      # See `build_hail_jar_and_wheel`
-      time retry make shadowJar
-      if [ ! -f out/hail/2.12/assembly.dest/out.jar ]; then
-          echo 'no out.jar found after mill assembly returned. going to sleep'
-          sleep 5
-      fi
-
-      time retry make wheel
-    inputs:
-      - from: /repo
-        to: /io/repo
-    outputs:
-      - from: /io/repo/hail/build/deploy/dist
-        to: /azure-wheel
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: buildImage2
-    name: hail_run_image
-    dockerFile: /io/repo/hail/Dockerfile.hail-run
-    contextPath: /io/repo
-    publishAs: hail-run
-    resources:
-      storage: 10Gi
-      cpu: "2"
-      memory: standard
-    inputs:
-      - from: /repo/hail/Dockerfile.hail-run
-        to: /io/repo/hail/Dockerfile.hail-run
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/repo/hail/python/dev/pinned-requirements.txt
-      - from: /repo/docker/core-site.xml
-        to: /io/repo/docker/core-site.xml
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: jvm_entryway_jar
-    image:
-      valueFrom: base_image.image
-    script: |
-      set -ex
-
-      cd /io/batch/jvm-entryway
-      time retry sh mill --no-daemon --version
-      sh mill --no-daemon assembly
-    inputs:
-      - from: /repo/batch
-        to: /io/batch
-    outputs:
-      - from: /io/batch/jvm-entryway/out/assembly.dest/out.jar
-        to: /jvm-entryway.jar
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: buildImage2
-    name: batch_worker_image
-    dockerFile: /io/repo/batch/Dockerfile.worker
-    contextPath: /io/repo
-    publishAs: batch-worker
-    inputs:
-      - from: /repo/letsencrypt/subdomains.txt
-        to: /io/repo/letsencrypt/subdomains.txt
-      - from: /repo/docker
-        to: /io/repo/docker
-      - from: /repo/batch
-        to: /io/repo/batch
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-      - from: /jvm-entryway.jar
-        to: /io/repo/batch/jvm-entryway/out/assembly.dest/out.jar
-    dependsOn:
-      - merge_code
-      - hail_ubuntu_image
-      - jvm_entryway_jar
-  - kind: runImage
-    name: upload_test_resources_to_blob_storage
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-      cd /io/repo/hail/
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      python3 -m hailtop.aiotools.copy 'null' '[
-      {"from": "hail/test/resources",
-       "to":   "{{ global.test_storage_uri }}/{{ token }}/test/resources"},
-      {"from": "python/hail/docs/data",
-       "to":   "{{ global.test_storage_uri }}/{{ token }}/doctest/data"}
-      ]'
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    inputs:
-      - from: /repo/hail/hail/test/resources
-        to: /io/repo/hail/hail/test/resources
-      - from: /repo/hail/python/hail/docs/data
-        to: /io/repo/hail/python/hail/docs/data
-    dependsOn:
-      - default_ns
-      - hailgenetics_hailtop_image
-      - create_test_gsa_keys
-      - merge_code
-  - kind: runImage
-    name: test_hail_java
-    numSplits: 5
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      mkdir -p hail/test
-      tar xzf resources.tar.gz -C hail/test
-      tar xzf splits.tar.gz
-      export HAIL_TEST_SKIP_R=1
-      java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-$HAIL_RUN_IMAGE_SPLIT_INDEX.xml
-    inputs:
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
-        to: /io/hail-test.jar
-      - from: /splits.tar.gz
-        to: /io/splits.tar.gz
-    outputs:
-      - from: /io/test-output
-        to: /test-output
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - hail_run_image
-      - create_test_gsa_keys
-      - build_debug_hail_test_jar
-      - build_hail_test_artifacts
-  - kind: runImage
-    name: test_hail_python
-    numSplits: 28
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      tar xzf test.tar.gz
-      tar xzf resources.tar.gz
-      tar xzf data.tar.gz
-      python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
-
-      # pyspark/conf/core-site.xml already points at /gsa-key/key.json
-      mv /test-gsa-key/key.json /gsa-key/key.json
-
-      export HAIL_QUERY_N_CORES=2
-      export OMP_NUM_THREADS=2
-      export OPENBLAS_NUM_THREADS=2
-      export MKL_NUM_THREADS=2
-      export VECLIB_MAXIMUM_THREADS=2
-      export NUMEXPR_NUM_THREADS=2
-
-      export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
-      export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
-      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
-      
-      python3 -m pytest \
-              -Werror:::hail -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --timeout=120 \
-              test/hail
-    inputs:
-      - from: /derived/debug/hail/build/deploy/dist
-        to: /io/debug-wheel
-      - from: /test.tar.gz
-        to: /io/test.tar.gz
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /data.tar.gz
-        to: /io/data.tar.gz
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - hail_run_image
-      - create_test_gsa_keys
-      - build_hail_debug_jar_and_wheel
-      - build_hail_test_artifacts
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_hailtop_python_fs
-    numSplits: 5
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      tar xzf test.tar.gz
-
-      python3 -m pip install -r test-requirements.txt
-
-      export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
-      export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
-
-      export HAIL_TEST_AZURE_ACCOUNT=hailtest
-      export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
-      # Required for SAS testing on Azure
-      export HAIL_TEST_AZURE_RESGRP=hail-dev
-      export HAIL_TEST_AZURE_SUBID=22cd45fe-f996-4c51-af67-ef329d977519
-      export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --timeout=120 \
-              test/hailtop/inter_cloud
-    timeout: 1200
-    inputs:
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/test-requirements.txt
-      - from: /test.tar.gz
-        to: /io/test.tar.gz
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-      - name: test-aws-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-aws-key
-      - name: test-azure-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-azure-key
-    dependsOn:
-      - default_ns
-      - hailgenetics_hailtop_image
-      - create_test_gsa_keys
-      - build_hail_test_artifacts
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_hail_python_unchecked_allocator
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      tar xzf test.tar.gz
-      tar xzf resources.tar.gz
-      tar xzf data.tar.gz
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      # pyspark/conf/core-site.xml already points at /gsa-key/key.json
-      mv /test-gsa-key/key.json /gsa-key/key.json
-
-      export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
-      export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
-      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              -m unchecked_allocator \
-              --ignore=test/hailtop/batch/ \
-              --ignore=test/hailtop/inter_cloud \
-              --timeout=120 \
-              test
-    inputs:
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-      - from: /test.tar.gz
-        to: /io/test.tar.gz
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /data.tar.gz
-        to: /io/data.tar.gz
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - hail_run_image
-      - build_hail_jar_and_wheel
-      - build_hail_test_artifacts
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_hail_python_local_backend
-    numSplits: 48
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      tar xzf test.tar.gz
-      tar xzf resources.tar.gz
-      tar xzf data.tar.gz
-      python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
-      mkdir -p /io/tmp
-
-      # The test should use the test credentials, not CI's credentials
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export HAIL_QUERY_N_CORES=2
-      export OMP_NUM_THREADS=2
-      export OPENBLAS_NUM_THREADS=2
-      export MKL_NUM_THREADS=2
-      export VECLIB_MAXIMUM_THREADS=2
-      export NUMEXPR_NUM_THREADS=2
-
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_TEST_STORAGE_URI=/io/tmp/
-      export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
-      export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
-      export HAIL_LOCAL_BACKEND_HEAP_SIZE=3G
-
-      hailctl config set query/backend local
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --ignore=test/hailtop/ \
-              --timeout=120 \
-              test
-    timeout: 1800
-    inputs:
-      - from: /derived/debug/hail/build/deploy/dist
-        to: /io/debug-wheel
-      - from: /test.tar.gz
-        to: /io/test.tar.gz
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /data.tar.gz
-        to: /io/data.tar.gz
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - hail_run_image
-      - create_test_gsa_keys
-      - build_hail_debug_jar_and_wheel
-      - build_hail_test_artifacts
-  - kind: runImage
-    name: test_python_docs
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      export HAIL_QUERY_N_CORES=2
-      export OMP_NUM_THREADS=2
-      export OPENBLAS_NUM_THREADS=2
-      export MKL_NUM_THREADS=2
-      export VECLIB_MAXIMUM_THREADS=2
-      export NUMEXPR_NUM_THREADS=2
-
-      export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
-      export HAIL_LOCATION=$(dirname $(python3 -c 'import hail; print(hail.__file__)'))
-
-      mv /io/docs $HAIL_LOCATION/docs
-
-      # NB: do not use --timeout with doctest because there is no way to override it.
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --doctest-modules \
-              --doctest-glob='*.rst' \
-              --doctest-continue-on-failure \
-              --ignore=$HAIL_LOCATION/test \
-              --ignore=$HAIL_LOCATION/docs/conf.py \
-              --ignore=$HAIL_LOCATION/docs/doctest_write_data.py \
-              --rootdir $HAIL_LOCATION \
-              $HAIL_LOCATION
-    inputs:
-      - from: /repo/hail/python/hail/docs
-        to: /io/docs
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-    dependsOn:
-      - build_hail_jar_and_wheel
-      - hail_run_image
-    clouds:
-      - gcp
-  - kind: runImage
-    name: make_docs
-    resources:
-      memory: standard
-      cpu: '4'
-    image:
-      valueFrom: hail_run_image.image
-    script: |
-      set -ex
-      set -o pipefail
-      export HAIL_USE_PRIVATE_LENS_DATA=1
-      export HAIL_SHORT_VERSION='0.2'
-      export SPHINXOPTS='-tgenerate_notebook_outputs'
-
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      cd /io/hail
-      export HAIL_WEBSITE_DIR=/io/website/website/
-
-      sed -E "s/\(hail\#([0-9]+)\)/(\[#\1](https:\/\/github.com\/hail-is\/hail\/pull\/\1))/g" \
-        < python/hail/docs/change_log.md \
-        | pandoc -o python/hail/docs/change_log.rst --fail-if-warnings --verbose
-
-      make -C python/hail/docs BUILDDIR=_build clean html
-      make -C python/hailtop/batch/docs BUILDDIR=_build clean html
-
-      mkdir -p www/docs
-      mv python/hail/docs/_build/html www/docs/0.2
-      mv python/hailtop/batch/docs/_build/html www/docs/batch
-
-      HAIL_CACHE_VERSION=$(cat env/HAIL_VERSION)
-      find www -iname *.html -type f -exec sed -i -e "s/\.css/\.css\?v\=$HAIL_CACHE_VERSION/" {} +;
-
-      tar czf /io/www.tar.gz www
-    inputs:
-      - from: /repo/hail
-        to: /io/hail
-      - from: /repo/website/website
-        to: /io/website/website
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-    outputs:
-      - from: /io/www.tar.gz
-        to: /www.tar.gz
-    dependsOn:
-      - merge_code
-      - build_hail_jar_and_wheel
-      - hail_run_image
-  - kind: buildImage2
-    name: hailgenetics_hail_image
-    dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
-    contextPath: /io/repo
-    publishAs: hailgenetics/hail
-    buildArgs:
-      - name: BASE_IMAGE
-        value:
-          valueFrom: hail_ubuntu_image.image
-      - name: HAIL_WHEEL_DIR
-        value: /wheel
-    inputs:
-      - from: /repo/docker/hailgenetics/hail
-        to: /io/repo/docker/hailgenetics/hail
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/wheel
-    dependsOn:
-      - merge_code
-      - build_hail_jar_and_wheel
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: hailgenetics_hail_image_python_3_10
-    dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
-    contextPath: /io/repo
-    publishAs: hailgenetics/hail
-    buildArgs:
-      - name: BASE_IMAGE
-        value:
-          valueFrom: hail_ubuntu_image_python_3_10.image
-      - name: HAIL_WHEEL_DIR
-        value: /wheel
-    inputs:
-      - from: /repo/docker/hailgenetics/hail
-        to: /io/repo/docker/hailgenetics/hail
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/wheel
-    dependsOn:
-      - merge_code
-      - build_hail_jar_and_wheel
-      - hail_ubuntu_image_python_3_10
-  - kind: buildImage2
-    name: hailgenetics_hail_image_python_3_12
-    dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
-    contextPath: /io/repo
-    publishAs: hailgenetics/hail
-    buildArgs:
-      - name: BASE_IMAGE
-        value:
-          valueFrom: hail_ubuntu_image_python_3_12.image
-      - name: HAIL_WHEEL_DIR
-        value: /wheel
-    inputs:
-      - from: /repo/docker/hailgenetics/hail
-        to: /io/repo/docker/hailgenetics/hail
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/wheel
-    dependsOn:
-      - merge_code
-      - build_hail_jar_and_wheel
-      - hail_ubuntu_image_python_3_12
-  - kind: buildImage2
-    name: hailgenetics_hail_image_python_3_13
-    dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
-    contextPath: /io/repo
-    publishAs: hailgenetics/hail
-    buildArgs:
-      - name: BASE_IMAGE
-        value:
-          valueFrom: hail_ubuntu_image_python_3_13.image
-      - name: HAIL_WHEEL_DIR
-        value: /wheel
-    inputs:
-      - from: /repo/docker/hailgenetics/hail
-        to: /io/repo/docker/hailgenetics/hail
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/wheel
-    dependsOn:
-      - merge_code
-      - build_hail_jar_and_wheel
-      - hail_ubuntu_image_python_3_13
-  - kind: runImage
-    name: test_hailgenetics_hail_image
-    image:
-      valueFrom: hailgenetics_hail_image.image
-    script: |
-      set -ex
-      python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 11, sys.version_info'
-      python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
-      python3 -c 'import numpy; import pandas; import sklearn; import scipy'
-    dependsOn:
-      - hailgenetics_hail_image
-  - kind: runImage
-    name: test_hailgenetics_hail_image_python_3_10
-    image:
-      valueFrom: hailgenetics_hail_image_python_3_10.image
-    script: |
-      set -ex
-      python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 10, sys.version_info'
-      python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
-      python3 -c 'import numpy; import pandas; import sklearn; import scipy'
-    dependsOn:
-      - hailgenetics_hail_image_python_3_10
-  - kind: runImage
-    name: test_hailgenetics_hail_image_python_3_12
-    image:
-      valueFrom: hailgenetics_hail_image_python_3_12.image
-    script: |
-      set -ex
-      python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 12, sys.version_info'
-      python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
-      python3 -c 'import numpy; import pandas; import sklearn; import scipy'
-    dependsOn:
-      - hailgenetics_hail_image_python_3_12
-  - kind: runImage
-    name: test_hailgenetics_hail_image_python_3_13
-    image:
-      valueFrom: hailgenetics_hail_image_python_3_13.image
-    script: |
-      set -ex
-      python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 13, sys.version_info'
-      python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
-      python3 -c 'import numpy; import pandas; import sklearn; import scipy'
-    dependsOn:
-      - hailgenetics_hail_image_python_3_13
-  - kind: buildImage2
-    name: hail_dev_image
-    dockerFile: /io/repo/docker/Dockerfile.hail-dev
-    contextPath: /io/repo
-    publishAs: hail-dev
-    inputs:
-      - from: /repo/docker/Dockerfile.hail-dev
-        to: /io/repo/docker/Dockerfile.hail-dev
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/repo/hail/python/dev/pinned-requirements.txt
-    dependsOn:
-      - hailgenetics_hail_image
-      - merge_code
-  - kind: buildImage2
-    name: hail_linting_image
-    contextPath: /io/repo
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
-        FROM $BASE_IMAGE
-        RUN hail-apt-get-install git make openjdk-11-jre-headless
-        COPY hail/python/pinned-requirements.txt hail-requirements.txt
-        COPY hail/python/dev/pinned-requirements.txt dev-requirements.txt
-        COPY gear/pinned-requirements.txt gear-requirements.txt
-        COPY web_common/pinned-requirements.txt web_common-requirements.txt
-        COPY batch/pinned-requirements.txt batch-requirements.txt
-        COPY ci/pinned-requirements.txt ci-requirements.txt
-        RUN python3 -m pip install \
-            -r hail-requirements.txt \
-            -r dev-requirements.txt \
-            -r gear-requirements.txt \
-            -r web_common-requirements.txt \
-            -r batch-requirements.txt \
-            -r ci-requirements.txt \
-            && \
-            python3 -m pyright --version # Force the installation of node and npm pyright in the image
-    publishAs: linting
-    inputs:
-      - from: /repo/hail/python/pinned-requirements.txt
-        to: /io/repo/hail/python/pinned-requirements.txt
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/repo/hail/python/dev/pinned-requirements.txt
-      - from: /repo/gear/pinned-requirements.txt
-        to: /io/repo/gear/pinned-requirements.txt
-      - from: /repo/web_common/pinned-requirements.txt
-        to: /io/repo/web_common/pinned-requirements.txt
-      - from: /repo/batch/pinned-requirements.txt
-        to: /io/repo/batch/pinned-requirements.txt
-      - from: /repo/ci/pinned-requirements.txt
-        to: /io/repo/ci/pinned-requirements.txt
-    dependsOn:
-      - merge_code
-      - hail_ubuntu_image
-  - kind: runImage
-    name: check_pip_requirements
-    image:
-      valueFrom: hail_linting_image.image
-    script: |
-      set -ex
-      cd /io/repo
-      chmod 755 ./check_pip_requirements.sh
-      make check-pip-requirements
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - hail_linting_image
-      - merge_code
-  - kind: runImage
-    name: check_services
-    image:
-      valueFrom: hail_linting_image.image
-    script: |
-      set -ex
-      cd /io/repo
-      {% if 'target_sha' in code %}
-      export HAIL_TARGET_SHA={{ code.target_sha }}
-      {% endif %}
-      make -k check-services
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - hail_linting_image
-      - merge_code
-  - kind: runImage
-    name: check_hail
-    image:
-      valueFrom: hail_linting_image.image
-    resources:
-      memory: 8G
-    script: |
-      set -ex
-      cd /io/repo
-      make check-hail
-    inputs:
-      - from: /repo/Makefile
-        to: /io/repo/Makefile
-      - from: /repo/pylintrc
-        to: /io/repo/pylintrc
-      - from: /repo/pyproject.toml
-        to: /io/repo/pyproject.toml
-      - from: /repo/hail
-        to: /io/repo/hail
-      - from: /repo/config.mk
-        to: /io/repo/config.mk
-    dependsOn:
-      - hail_linting_image
-      - merge_code
-  - kind: runImage
-    name: compile_hail_213
-    image:
-      valueFrom: base_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io/repo/hail
-
-      HAIL_BUILD_MODE='CI'
-      time retry sh mill --no-daemon hail[2.13].__.compile
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - base_image
-      - merge_code
-  - kind: runImage
-    name: get_pip_versioned_docs
-    image:
-      valueFrom: hailgenetics_hail_image.image
-    script: |
-      set -ex
-
-      cd /io/repo
-
-      # dev deploy elides the hail-is remote, add it and retrieve the tags
-      git remote add hail-is https://github.com/hail-is/hail.git
-
-      export HAIL_PIP_VERSION=$(cat hail/env/HAIL_PIP_VERSION)
-
-      if git ls-remote --exit-code --tags hail-is $HAIL_PIP_VERSION
-      then
-        # In this case, we want to get the docs from Google Storage.
-        python3 -m hailtop.aiotools.copy 'null' '[
-        {"from": "gs://hail-common/website/'$HAIL_PIP_VERSION'/www.tar.gz",
-        "to": "www.tar.gz"}
-        ]'
-      else
-        cp /io/www.tar.gz .
-      fi
-
-      mkdir -p hail/build/www/docs/0.2
-      tar -xvf www.tar.gz -C hail/build/www/docs --strip-components 2 --no-same-owner
-
-      python3 -m hailtop.aiotools.copy 'null' '[
-      {"from": "gs://hail-common/builds/0.1/docs/hail-0.1-docs-5a6778710097.tar.gz",
-       "to": "hail-0.1-docs-5a6778710097.tar.gz"}
-      ]'
-
-      mkdir -p hail/build/www/docs/0.1
-      tar -xvf hail-0.1-docs-5a6778710097.tar.gz -C hail/build/www/docs/0.1 --strip-components 2 --no-same-owner
-
-      tar czf /io/docs.tar.gz -C hail/build/www .
-    resources:
-      memory: standard
-      cpu: '2'
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /www.tar.gz
-        to: /io/www.tar.gz
-    outputs:
-      - from: /io/docs.tar.gz
-        to: /docs.tar.gz
-    dependsOn:
-      - hailgenetics_hail_image
-      - merge_code
-      - make_docs
-    clouds:
-      - gcp
-  - kind: deploy
-    name: deploy_grafana
+    name: auth
+  dependsOn:
+  - default_ns
+  - merge_code
+  - delete_auth_tables
+  - ci_utils_image
+  - create_test_database_server_config
+  - deploy_test_db
+- kind: runImage
+  name: create_deploy_config
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+
+    # k8s deploy config
+    {% if default_ns.name == "default" %}
+    cat > deploy-config.json <<EOF
+    {"location":"k8s","default_namespace":"{{ default_ns.name }}","domain":"{{ global.domain }}"}
+    EOF
+    {% else %}
+    cat > deploy-config.json <<EOF
+    {"location":"k8s","default_namespace":"{{ default_ns.name }}","domain":"internal.{{ global.domain }}","base_path":"/{{ default_ns.name }}"}
+    EOF
+    {% endif %}
+    kubectl -n {{ default_ns.name }} create secret generic deploy-config \
+            --from-file=./deploy-config.json \
+            --save-config --dry-run=client -o yaml \
+        | kubectl -n {{ default_ns.name }} apply -f -
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: grafana/deployment.yaml
-    scopes:
-      - deploy
-      - test
-      - dev
-    dependsOn:
-      - default_ns
-      - hail_ubuntu_image
-      - create_certs
-      - copy_third_party_images
-  - kind: deploy
-    name: deploy_prometheus
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+- kind: deploy
+  name: deploy_admin_pod
+  namespace:
+    valueFrom: default_ns.name
+  config: admin-pod/admin-pod.yaml
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - admin_pod_image
+  - create_deploy_config
+  - create_certs
+- kind: runImage
+  name: create_session_key
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    # create session keys
+    N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers session-secret-key | wc -l | tr -d '[:space:]')
+    if [[ $N != 0 ]]; then
+      exit
+    fi
+    mkdir /session-secret-key
+    cat > generate-session-key.py <<EOF
+    import base64
+    from cryptography import fernet
+    with open('/session-secret-key/session-secret-key', 'wb') as f:
+        f.write(base64.urlsafe_b64decode(fernet.Fernet.generate_key()))
+    EOF
+    python3 generate-session-key.py
+    kubectl -n {{ default_ns.name }} create secret generic session-secret-key --from-file=/session-secret-key/session-secret-key
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: prometheus/prometheus.yaml
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - create_certs
-      - copy_third_party_images
-  - kind: deploy
-    name: deploy_auth
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+- kind: runImage
+  name: create_test_gsa_keys
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    kubectl -n {{ default_ns.name }} get -o json secret testns-test-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "test-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+    kubectl -n {{ default_ns.name }} get -o json secret testns-test-dev-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "test-dev-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+    kubectl -n {{ default_ns.name }} get -o json secret testns-auth-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "auth-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+    kubectl -n {{ default_ns.name }} get -o json secret testns-batch-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "batch-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+    kubectl -n {{ default_ns.name }} get -o json secret testns-ci-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "ci-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+    kubectl -n {{ default_ns.name }} get -o json secret testns-grafana-gsa-key | jq '{apiVersion, kind, type, data, metadata: {name: "grafana-gsa-key"}}' | kubectl -n {{ default_ns.name }} apply -f -
+  scopes:
+  - test
+  - dev
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    config: auth/deployment.yaml
-    wait:
-      - kind: Service
-        name: auth
-        for: alive
-      - kind: Service
-        name: auth-driver
-        for: alive
-    dependsOn:
-      - default_ns
-      - create_deploy_config
-      - create_session_key
-      - auth_database
-      - auth_image
-      - create_certs
-      - create_accounts
-  - kind: runImage
-    name: create_initial_user
-    runIfRequested: true
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-
-      {% if default_ns.name == "default" %}
-      hailctl auth create-user --developer {{ code.username }} {{ code.login_id }}
-      {% else %}
-      hailctl auth create-user \
-        --developer \
-        --hail-identity {{ code.hail_identity }} \
-        --hail-credentials-secret-name {{ code.username }}-gsa-key \
-        {{ code.username }} {{ code.login_id }}
-      {% endif %}
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    dependsOn:
-      - default_ns
-      - hailgenetics_hailtop_image
-      - merge_code
-      - deploy_auth
-  - kind: runImage
-    name: delete_monitoring_tables
-    image:
-      valueFrom: monitoring_image.image
-    script: |
-      set -ex
-      cd /io
-      python3 delete_dev_database.py {{ default_ns.name }} monitoring
-    inputs:
-      - from: /repo/ci/delete_dev_database.py
-        to: /io/delete_dev_database.py
-    secrets:
-      - name: database-server-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /sql-config
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    network: private
-    runIfRequested: true
-    scopes:
-      - dev
-    dependsOn:
-      - default_ns
-      - monitoring_image
-      - merge_code
-      - create_test_database_server_config
-  - kind: createDatabase2
-    name: monitoring_database
-    databaseName: monitoring
-    image:
-      valueFrom: ci_utils_image.image
-    migrations:
-      - name: initial
-        script: /io/sql/000-initial.sql
-    inputs:
-      - from: /repo/monitoring/sql
-        to: /io/sql
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+- kind: deploy
+  name: deploy_auth_driver_service_account
+  namespace:
+    valueFrom: default_ns.name
+  config: auth/auth-driver-service-account.yaml
+  dependsOn:
+  - default_ns
+- kind: runImage
+  name: create_accounts
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: auth_image.image
+  script: |
+    set -ex
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_SCOPE={{ scope }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/auth-gsa-key/key.json
+
+    python3 /io/bootstrap_create_accounts.py
+  serviceAccount:
+    name: admin
     namespace:
       valueFrom: default_ns.name
-    shutdowns:
-      - kind: Deployment
-        namespace:
-          valueFrom: default_ns.name
-        name: monitoring
-    dependsOn:
-      - default_ns
-      - merge_code
-      - delete_monitoring_tables
-      - ci_utils_image
-      - create_test_database_server_config
-      - deploy_test_db
-  - kind: deploy
-    name: deploy_monitoring
+  network: private
+  secrets:
+  - name:
+      valueFrom: auth_database.user_secret_name
     namespace:
       valueFrom: default_ns.name
-    config: monitoring/deployment.yaml
-    wait:
-      - kind: Service
-        name: monitoring
-        for: alive
-    dependsOn:
-      - default_ns
-      - monitoring_image
-      - monitoring_database
-      - deploy_auth
-      - create_certs
-      - create_accounts
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_monitoring
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: hail_dev_image.image
-    script: |
-      set -ex
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --timeout=120 \
-              /io/monitoring/test
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    timeout: 300
-    inputs:
-      - from: /repo/monitoring/test
-        to: /io/monitoring/test
-    dependsOn:
-      - hail_dev_image
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - create_certs
-      - deploy_monitoring
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_auth_copy_paste_login
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-
-      # Or else hailctl will try to authenticate as CI
-      unset HAIL_IDENTITY_PROVIDER_JSON
-
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json
-
-      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
-                         auth /api/v1alpha/copy-paste-token \
-                         -fsSL \
-                         --retry 10 \
-                         --retry-delay 5 \
-                         -XPOST)
-      hailctl auth copy-paste-login "$COPY_PASTE_TOKEN"
-
-      if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN"
-      then
-          echo "reusing a token should not work, but did"
-          exit 1
-      fi
-
-      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
-                         auth /api/v1alpha/copy-paste-token \
-                         -fsSL \
-                         --retry 3 \
-                         --retry-delay 5 \
-                         -XPOST)
-      python3 -c '
-      from hailtop.auth import copy_paste_login;
-      copy_paste_login("'$COPY_PASTE_TOKEN'")
-      '
-
-      python3 -c '
-      from hailtop.auth import copy_paste_login;
-      import aiohttp
-      try:
-          copy_paste_login("'$COPY_PASTE_TOKEN'")
-          print("reusing a token should not work, but did")
-          sys.exit(1)
-      except aiohttp.client_exceptions.ClientResponseError as exc:
-          assert(exc.status == 401)
-      '
-    secrets:
-      - name: test-tokens
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /user-tokens
-    dependsOn:
-      - default_ns
-      - create_accounts
-      - deploy_auth
-      - create_deploy_config
-      - hailgenetics_hailtop_image
-  - kind: runImage
-    name: test_auth_copy_paste_login_timeout
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-
-      # Or else hailctl will try to authenticate as CI
-      unset HAIL_IDENTITY_PROVIDER_JSON
-
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json
-
-      COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
-                         auth /api/v1alpha/copy-paste-token \
-                         -fsSL \
-                         --retry 10 \
-                         --retry-delay 5 \
-                         -XPOST)
-      sleep $(( 5 * 60 + 1))
-      if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN" --namespace {{ default_ns.name }}
-      then
-          echo "using an expired token should not work, but did"
-          exit 1
-      fi
-
-      python3 -c '
-      import aiohttp
-      from hailtop.auth import copy_paste_login;
-      try:
-          copy_paste_login("'$COPY_PASTE_TOKEN'")
-          print("using an expired token should not work, but did")
-          sys.exit(1)
-      except aiohttp.client_exceptions.ClientResponseError as exc:
-          assert(exc.status == 401)
-      '
-    secrets:
-      - name: test-tokens
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /user-tokens
-    dependsOn:
-      - default_ns
-      - create_accounts
-      - deploy_auth
-      - create_deploy_config
-      - hailgenetics_hailtop_image
-  - kind: runImage
-    name: delete_batch_tables
-    image:
-      valueFrom: batch_image.image
-    script: |
-      set -ex
-      cd /io
-      python3 delete_dev_database.py {{ default_ns.name }} batch
-    inputs:
-      - from: /repo/ci/delete_dev_database.py
-        to: /io/delete_dev_database.py
-    secrets:
-      - name: database-server-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /sql-config
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    network: private
-    runIfRequested: true
-    scopes:
-      - dev
-    dependsOn:
-      - default_ns
-      - batch_image
-      - merge_code
-      - create_test_database_server_config
-  - kind: runImage
-    name: delete_ci_tables
-    image:
-      valueFrom: ci_image.image
-    script: |
-      set -ex
-      cd /io
-      python3 delete_dev_database.py {{ default_ns.name }} ci
-    inputs:
-      - from: /repo/ci/delete_dev_database.py
-        to: /io/delete_dev_database.py
-    secrets:
-      - name: database-server-config
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /sql-config
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    network: private
-    runIfRequested: true
-    scopes:
-      - dev
-    dependsOn:
-      - default_ns
-      - ci_image
-      - merge_code
-      - create_test_database_server_config
-  - kind: createDatabase2
-    name: ci_database
-    databaseName: ci
-    image:
-      valueFrom: ci_utils_image.image
-    migrations:
-      - name: initial
-        script: /io/sql/000-initial.sql
-      - name: invalidated-batches
-        script: /io/sql/001-invalidated-batches.sql
-      - name: add-frozen-mode
-        script: /io/sql/002-add-frozen-mode.sql
-        online: true
-      - name: active-namespaces
-        script: /io/sql/003-active-namespaces.sql
-        online: true
-      - name: fix-default-namespace-record
-        script: /io/sql/004-fix-default-namespace.py
-        online: true
-      - name: record-failure-notifications
-        script: /io/sql/005-record-failure-notifications.sql
-        online: true
-      - name: add-service-rate-limits
-        script: /io/sql/006-add-service-rate-limits.sql
-        online: true
-    inputs:
-      - from: /repo/ci/sql
-        to: /io/sql
+    mountPath: /sql-config
+  - name: database-server-config
     namespace:
       valueFrom: default_ns.name
-    shutdowns:
-      - kind: Deployment
-        namespace:
-          valueFrom: default_ns.name
-        name: ci
-    dependsOn:
-      - default_ns
-      - merge_code
-      - delete_ci_tables
-      - ci_utils_image
-      - create_test_database_server_config
-      - deploy_test_db
-  - kind: createDatabase2
-    name: batch_database
-    databaseName: batch
-    image:
-      valueFrom: ci_utils_image.image
-    migrations:
-      - name: initial
-        script: /io/sql/000-initial.sql
-      - name: insert-globals
-        script: /io/sql/001-insert_globals.py
-      - name: create-billing-projects
-        script: /io/sql/002-create-billing-projects.sql
-      - name: increase-spec-size
-        script: /io/sql/003-increase-spec-size.sql
-      - name: remove-fk-batches-user-resources
-        script: /io/sql/004-remove-fk-batches-user-resources.sql
-      - name: change-ready-cores-bigint
-        script: /io/sql/005-change-ready-cores-bigint.sql
-      - name: add-user-resources-ready-cores-token
-        script: /io/sql/006-add-user-resources-ready-cores-token.sql
-      - name: add-lock-in-share-mode
-        script: /io/sql/007-add-lock-in-share-mode.sql
-      - name: add-batch-create-token
-        script: /io/sql/008-add-batch-create-token.sql
-      - name: improve-cancel
-        script: /io/sql/009-improve-cancel.sql
-      - name: store-specs-in-gcs
-        script: /io/sql/010-store-specs-in-gcs.sql
-      - name: add-batches-time-closed
-        script: /io/sql/011-add-batches-time-closed.sql
-      - name: add-instance-zone
-        script: /io/sql/012-add-instance-zone.sql
-      - name: add-batches-time-created-index
-        script: /io/sql/013-add-batches-time-created-index.sql
-      - name: change-test-worker-disk-size
-        script: /io/sql/014-change_test_worker_disk_size.py
-      - name: add-resources
-        script: /io/sql/015-add-resources.sql
-      - name: insert-resources
-        script: /io/sql/016-insert_resources.py
-      - name: insert-standing-worker-globals
-        script: /io/sql/017-insert_standing_worker_globals.py
-      - name: insert-local-ssd-resource
-        script: /io/sql/018-insert_local_ssd_resource.py
-      - name: fix-mark-job-complete-on-error
-        script: /io/sql/019-fix-mark-job-complete-on-error.sql
-      - name: add-worker-pd-ssd-data-disk
-        script: /io/sql/020-add-worker-pd-ssd-data-disk.sql
-      - name: add-aggregated-batch-resources-tokens
-        script: /io/sql/021-add-aggregated-batch-resources-tokens.sql
-      - name: change-test-worker-pool-size
-        script: /io/sql/022-change_test_worker_pool_size.py
-      - name: add-test-dev-to-billing-project-users
-        script: /io/sql/023-add-test-dev-to-billing-project-users.sql
-      - name: add-status-flag-billing-projects
-        script: /io/sql/024-add-status-flag-billing-projects.sql
-      - name: add-aggregated-billing-project-resources
-        script: /io/sql/025-add-aggregated-billing-project-resources.sql
-      - name: add-enable-standing-worker
-        script: /io/sql/026-add-enable-standing-worker.py
-      - name: add-inst-colls
-        script: /io/sql/027-add-inst-colls.sql
-      - name: add-creating-job-state
-        script: /io/sql/028-add-creating-job-state.sql
-      - name: add-job-private-inst-coll
-        script: /io/sql/029-add-job-private-inst-coll.sql
-      - name: insert-nonpreemptible-resources
-        script: /io/sql/030-insert_nonpreemptible_resources.py
-      - name: fix-schedule-job
-        script: /io/sql/031-fix-schedule-job.sql
-      - name: increase-test-and-dev-pool-sizes
-        script: /io/sql/032-increase-test-and-dev-pool-sizes.py
-      - name: fix-provisioning-bug
-        script: /io/sql/033-fix-provisioning-bug.sql
-      - name: do-not-lock-entire-batch
-        script: /io/sql/034-do-not-lock-entire-batch.sql
-      - name: add-fail-fast
-        script: /io/sql/035-add-fail-fast.sql
-      - name: add-frozen-mode
-        script: /io/sql/036-add-frozen-mode.sql
-      - name: add-instance-config
-        script: /io/sql/037-add-instance-config.sql
-      - name: cloud-agnostic
-        script: /io/sql/038-cloud-agnostic.sql
-      - name: support-azure
-        script: /io/sql/039-support-azure.sql
-      - name: add-azure-tables
-        script: /io/sql/040-add_azure_tables.py
-      - name: change-azure-test-highcpu-pool
-        script: /io/sql/041-change_azure_test_highcpu_pool.py
-      - name: add-latest-product-versions
-        script: /io/sql/042-add-latest-product-versions.sql
-      - name: add-products-and-versions
-        script: /io/sql/043-add_products_and_versions.py
-      - name: kill-more-deadlocks
-        script: /io/sql/044-kill-more-deadlocks.sql
-      - name: kill-more-deadlocks2
-        script: /io/sql/045-kill-more-deadlocks2.sql
-      - name: no-locks-add-attempt
-        script: /io/sql/046-no-locks-add-attempt.sql
-      - name: fix-n-cancelled-creating-jobs
-        script: /io/sql/047-fix-n-cancelled-creating-jobs.sql
-      - name: big-test-instances
-        script: /io/sql/048-big-test-instances.py
-      - name: kill-mjc-deadlocks
-        script: /io/sql/049-kill-mjc-deadlocks.sql
-      - name: add-nonpreemptible-pools
-        script: /io/sql/050-add-nonpreemptible-pools.sql
-      - name: add-pool-label
-        script: /io/sql/050a-add-pool-label.sql
-      - name: set-test-and-dev-pools-to-8-core-max-2
-        script: /io/sql/051-set-test-and-dev-pools-to-8-core-max-2.py
-      - name: set-test-and-dev-jpim-to-max-5
-        script: /io/sql/052-set-test-and-dev-jpim-to-max-5.py
-        online: true
-      - name: minimize-deadlock-errors
-        script: /io/sql/053-minimize-deadlock-errors.sql
-        online: true
-      - name: add-resource-ids-sql
-        script: /io/sql/054-add-resource-ids.sql
-        online: true
-      - name: add-resource-ids-python
-        script: /io/sql/055-add_resource_ids.py
-        online: true
-      - name: modify-resource-id-trigger
-        script: /io/sql/056-modify-resource-id-trigger.sql
-        online: true
-      - name: rm-resource-names-agg-resources
-        script: /io/sql/057-rm-resource-names-agg-resources.sql
-        online: true
-      - name: rm-resource-foreign-keys
-        script: /io/sql/058-rm-resource-foreign-keys.py
-        online: true
-      - name: rm-resource-names-agg-resources-pt-2
-        script: /io/sql/059-rm-resource-names-agg-resources-pt-2.sql
-        online: true
-      - name: add-att-resources-format-version-lt-3
-        script: /io/sql/060-add-att-resources-format-version-lt-3.sql
-        online: true
-      - name: insert-attempt-resources-format-version-lt-3
-        script: /io/sql/061-insert_attempt_resources_format_version_lt_3.py
-        online: true
-      - name: revert-attempt-resources-trigger-back-compat
-        script: /io/sql/062-revert-attempt-resources-trigger-back-compat.sql
-        online: true
-      - name: add-agg-billing-by-date
-        script: /io/sql/063-add-agg-billing-by-date.sql
-        online: true
-      - name: populate-agg-billing-by-date
-        script: /io/sql/064-populate_agg_billing_by_date.py
-        online: true
-      - name: revert-temp-agg-by-date-infra
-        script: /io/sql/065-revert-temp-agg-by-date-infra.sql
-        online: true
-      - name: rename-timestamp-to-date
-        script: /io/sql/066-rename-timestamp-to-date.sql
-        online: true
-      - name: add-real-time-billing
-        script: /io/sql/067-add-real-time-billing.sql
-        online: true
-      - name: add-batch-updates
-        script: /io/sql/068-add-batch-updates.sql
-        online: true
-      - name: populate-batch-updates
-        script: /io/sql/069-populate_batch_updates.py
-        online: true
-      - name: cleanup-add-batch-updates
-        script: /io/sql/070-cleanup-add-batch-updates.sql
-        online: true
-      - name: add-jobs-update-id-index
-        script: /io/sql/071-add-jobs-update-id-index.sql
-        online: true
-      - name: no-dev-standing-workers-by-default
-        script: /io/sql/072-no_dev_standing_workers_by_default.py
-        online: true
-      - name: add-commit-updates
-        script: /io/sql/073-add-commit-updates.sql
-        online: true
-      - name: add-job-regions
-        script: /io/sql/074-add-job-regions.sql
-        online: true
-      - name: faster-regions-pool-scheduler
-        script: /io/sql/075-faster-regions-pool-scheduler.sql
-        online: true
-      - name: add-batch-state-index
-        script: /io/sql/076-add-batch-state-index.sql
-        online: true
-      - name: case-sensitive-billing-project
-        script: /io/sql/077-case-sensitive-billing-project.sql
-        online: true
-      - name: driver-behavior
-        script: /io/sql/078-driver_behavior.py
-        online: true
-      - name: cleanup-old-billing-tables
-        script: /io/sql/079-cleanup-old-billing-tables.sql
-        online: true
-      - name: add-deduped-resource-ids-to-resources
-        script: /io/sql/080-add-deduped-resource-ids-to-resources.sql
-        online: true
-      - name: create-resource-dedup-mapping
-        script: /io/sql/081-create_resource_dedup_mapping.py
-        online: true
-      - name: config-pool-min-instances
-        script: /io/sql/082-config-pool-min-instances.sql
-        online: true
-      - name: add-deduped-resource-ids-to-attempt-resources
-        script: /io/sql/083-add-deduped-resource-ids-to-attempt-resources.sql
-        online: true
-      - name: setup-deduped-resources-migration
-        script: /io/sql/084-setup-deduped-resources-migration.sql
-        online: true
-      - name: dedup-attempt-resources
-        script: /io/sql/085-dedup_attempt_resources.py
-        online: true
-      - name: mitigate-bad-attempt-resources-trigger
-        script: /io/sql/086-mitigate-bad-attempt-resources-trigger.sql
-        online: true
-      - name: set-test-and-dev-pools-to-16-core-max-3
-        script: /io/sql/087-set-test-and-dev-pools-to-16-core-max-3.py
-        online: true
-      - name: fix-billing-triggers-deduped-resource-id
-        script: /io/sql/088-fix-billing-triggers-deduped-resource-id.sql
-        online: true
-      - name: set-test-and-dev-pools-to-max-16-standing-16
-        script: /io/sql/089-set-test-and-dev-pools-to-max-16-standing-16.py
-        online: true
-      - name: set-test-min-pool-size-to-1
-        script: /io/sql/090-set-test-min-pool-size-to-1.py
-        online: true
-      - name: dedup-billing-project-users-v2
-        script: /io/sql/091-dedup_billing_project_users_v2.py
-        online: true
-      - name: list-jobs-extra-indices
-        script: /io/sql/092-list-jobs-extra-indices.sql
-        online: true
-      - name: dedup-billing-project-users-by-date
-        script: /io/sql/093-dedup_billing_project_users_by_date.py
-        online: true
-      - name: add-jobs-ready-time
-        script: /io/sql/094-add-jobs-ready-time.sql
-        online: true
-      - name: add-list-batches-index
-        script: /io/sql/095-add-list-batches-index.sql
-        online: true
-      - name: add-feature-flags
-        script: /io/sql/096-add-feature-flags.sql
-        online: true
-      - name: add-oms-agent-flag
-        script: /io/sql/097-add-oms-agent-flag.sql
-        online: true
-      - name: increase-test-max-idle-time
-        script: /io/sql/098-increase_test_max_idle_time.py
-        online: true
-      - name: turn_off_oms_agent_test_dev
-        script: /io/sql/099-turn_off_oms_agent_test_dev.py
-        online: true
-      - name: add-billing-index-token
-        script: /io/sql/100-add-billing-index-token.sql
-        online: true
-      - name: jobs-after-update-simple.sql
-        script: /io/sql/101-jobs-after-update-simple.sql
-        online: true
-      - name: turn-on-billing-compaction
-        script: /io/sql/102-turn_on_billing_compaction.py
-        online: true
-      - name: cleanup-deprecated-functions
-        script: /io/sql/103-cleanup-deprecated-functions.sql
-        online: true
-      - name: set-test-pools-to-known-parameters
-        script: /io/sql/104-set-test-pools-to-known-parameters.py
-        online: true
-      - name: add-gcp-support-logs-specs-and-firewall-fees
-        script: /io/sql/105-add-gcp-support-logs-specs-and-firewall-fees.py
-        online: true
-      - name: add-product-sku
-        script: /io/sql/106-add-product-sku.sql
-        online: true
-      - name: dedup-agg-batch-resources
-        script: /io/sql/107-dedup_agg_batch_resources.py
-        online: true
-      - name: setup-job-groups
-        script: /io/sql/108-setup-job-groups.sql
-        online: true
-      - name: dedup-job-resources
-        script: /io/sql/109-dedup_job_resources.py
-        online: true
-      - name: fix-job-groups-state-enum
-        script: /io/sql/110-fix-job-groups-state-enum.sql
-        online: true
-      - name: populate-job-groups
-        script: /io/sql/111-populate_job_groups.py
-        online: true
-      - name: rename-job-groups-tables
-        script: /io/sql/112-rename-job-groups-tables.sql
-        online: false  # this must be offline
-      - name: remove-v2-billing-writes
-        script: /io/sql/113-remove-v2-billing-writes.sql
-        online: true
-      - name: update-ip-fee-resource
-        script: /io/sql/114-update-ip-fee-resource.py
-        online: true
-      - name: remove-v2-billing-tables
-        script: /io/sql/115-remove-v2-billing-tables.sql
-        online: true
-      - name: finalize-job-groups
-        script: /io/sql/116-finalize-job-groups.sql
-        online: true
-      - name: fix-mark-job-complete-deadlocks
-        script: /io/sql/117-fix-mark-job-complete-deadlocks.sql
-        online: true
-      - name: jobs-add-n-max-attempts
-        script: /io/sql/118-jobs-add-n-max-attempts.sql
-        online: true
-      - name: is-job-cancelled
-        script: /io/sql/119-is-job-cancelled.sql
-    inputs:
-      - from: /repo/batch/sql
-        to: /io/sql
+    mountPath: /database-server-config
+  - name: auth-gsa-key
     namespace:
       valueFrom: default_ns.name
-    shutdowns:
-      - kind: Deployment
-        namespace:
-          valueFrom: default_ns.name
-        name: batch
-      - kind: Deployment
-        namespace:
-          valueFrom: default_ns.name
-        name: batch-driver
-    dependsOn:
-      - default_ns
-      - merge_code
-      - delete_batch_tables
-      - ci_utils_image
-      - create_test_database_server_config
-      - deploy_test_db
-  - kind: deploy
-    name: deploy_batch
+    mountPath: /auth-gsa-key
+  - name: global-config
     namespace:
       valueFrom: default_ns.name
-    config: batch/deployment.yaml
-    wait:
-      - kind: Service
-        name: batch
-        for: alive
-      - kind: Service
-        name: batch-driver
-        for: alive
-    dependsOn:
-      - default_ns
-      - deploy_batch_sa
-      - create_accounts
-      - batch_image
-      - batch_worker_image
-      - batch_database
-      - deploy_auth
-      - create_certs
-  - kind: runImage
-    name: add_developers
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      {% for user in code.get("developers", []) %}
-      {% if user['username'] != 'test-dev' %}
-      hailctl auth create-user \
-        --developer \
-        --hail-identity {{ user["hail_identity"] }} \
-        --hail-credentials-secret-name {{ user["username"] }}-gsa-key \
-        {{ user["username"] }} {{ user["login_id"] }}
-      {% endif %}
-      {% endfor %}
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    scopes:
-      - dev
-      - test
-    dependsOn:
-      - default_ns
-      - hailgenetics_hailtop_image
-      - deploy_batch
-  - kind: runImage
-    name: upload_query_jar
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-      export GOOGLE_APPLICATION_CREDENTIALS=/batch-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/batch-gsa-key/key.json
-
-      {% if deploy %}
-      HAIL_QUERY_JAR_URL={{ global.query_storage_uri }}
-      {% else %}
-      HAIL_QUERY_JAR_URL={{ global.test_storage_uri }}/{{ default_ns.name }}
-      {% endif %}
-      HAIL_QUERY_JAR_URL=${HAIL_QUERY_JAR_URL}/jars/$(cat /io/REVISION).jar
-
-      python3 -m hailtop.aiotools.copy 'null' '[{"from": "/io/hail.jar", "to": "'${HAIL_QUERY_JAR_URL}'"}]'
-    secrets:
-      - name: batch-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /batch-gsa-key
-    inputs:
-      - from: /derived/release/hail/out/hail/2.12/assembly.dest/out.jar
-        to: /io/hail.jar
-      - from: /repo/hail/env/REVISION
-        to: /io/REVISION
-    dependsOn:
-      - default_ns
-      - deploy_batch
-      - hailgenetics_hailtop_image
-      - build_hail_jar_and_wheel
-      - merge_code
-      - create_test_gsa_keys
-  - kind: runImage
-    name: test_hail_python_service_backend_gcp
-    numSplits: 16
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      cpu: '0.25'
-      preemptible: False
-    script: |
-      set -ex
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      cd /io/repo/hail/python
-
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
-      export HAIL_TEST_RESOURCES_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/test/resources/"
-      export HAIL_DOCTEST_DATA_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/doctest/data/"
-      export HAIL_GENETICS_VEP_GRCH37_85_IMAGE={{ hailgenetics_vep_grch37_85_image.image }}
-      export HAIL_GENETICS_VEP_GRCH38_95_IMAGE={{ hailgenetics_vep_grch38_95_image.image }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export GCS_REQUESTER_PAYS_PROJECT=broad-ctsa
-
-      export HAIL_SHUFFLE_MAX_BRANCH=4
-      export HAIL_SHUFFLE_CUTOFF=1000000
-      export HAIL_QUERY_BACKEND=batch
-      export HAIL_BATCH_REGIONS={{ global.gcp_region }}
-      export HAIL_BATCH_BILLING_PROJECT=test
-      export HAIL_BATCH_REMOTE_TMPDIR={{ global.test_storage_uri }}
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --ignore=test/hailtop/ \
-              --ignore=test/hail/matrixtable/test_file_formats.py \
-              -m backend \
-              --timeout=600 \
-              test
-    timeout: 5400
-    inputs:
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-      - from: /repo/hail/python/pytest.ini
-        to: /io/repo/hail/python/pytest.ini
-      - from: /repo/hail/python/test
-        to: /io/repo/hail/python/test
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - merge_code
-      - deploy_batch
-      - create_deploy_config
-      - create_accounts
-      - hail_run_image
-      - upload_query_jar
-      - upload_test_resources_to_blob_storage
-      - build_hail_jar_and_wheel
-      - hailgenetics_vep_grch37_85_image
-      - hailgenetics_vep_grch38_95_image
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_hail_python_service_backend_azure
-    numSplits: 16
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      cpu: '0.25'
-      preemptible: False
-    script: |
-      set -ex
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      cd /io/repo/hail/python
-
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
-      export HAIL_TEST_RESOURCES_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/test/resources/"
-      export HAIL_DOCTEST_DATA_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/doctest/data/"
-      export HAIL_GENETICS_VEP_GRCH37_85_IMAGE={{ hailgenetics_vep_grch37_85_image.image }}
-      export HAIL_GENETICS_VEP_GRCH38_95_IMAGE={{ hailgenetics_vep_grch38_95_image.image }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export HAIL_AZURE_SUBSCRIPTION_ID={{ global.azure_subscription_id }}
-      export HAIL_AZURE_RESOURCE_GROUP={{ global.azure_resource_group }}
-
-      export HAIL_SHUFFLE_MAX_BRANCH=4
-      export HAIL_SHUFFLE_CUTOFF=1000000
-      export HAIL_QUERY_BACKEND=batch
-      export HAIL_BATCH_REGIONS={{ global.azure_location }}
-      export HAIL_BATCH_BILLING_PROJECT=test
-      export HAIL_BATCH_REMOTE_TMPDIR={{ global.test_storage_uri }}
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --ignore=test/hailtop/ \
-              --ignore=test/hail/matrixtable/test_file_formats.py \
-              -m backend \
-              --timeout=600 \
-              test
-    timeout: 5400
-    inputs:
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-      - from: /repo/hail/python/pytest.ini
-        to: /io/repo/hail/python/pytest.ini
-      - from: /repo/hail/python/test
-        to: /io/repo/hail/python/test
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - merge_code
-      - deploy_batch
-      - create_deploy_config
-      - create_accounts
-      - hail_run_image
-      - upload_query_jar
-      - upload_test_resources_to_blob_storage
-      - build_hail_jar_and_wheel
-      - hailgenetics_vep_grch37_85_image
-      - hailgenetics_vep_grch38_95_image
-    scopes:
-      - deploy
-      - dev
-    clouds:
-      - azure
-  - kind: runImage
-    name: test_hail_spark_conf_requester_pays_parsing
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      cpu: '0.5'
-      preemptible: False
-    script: |
-      set -ex
-      python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
-
-      export YOU_MAY_OVERWRITE_MY_SPARK_DEFAULTS_CONF_AND_HAILCTL_SETTINGS=1
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              /io/test_requester_pays_parsing.py
-    inputs:
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-      - from: /repo/hail/scripts/test_requester_pays_parsing.py
-        to: /io/test_requester_pays_parsing.py
-    dependsOn:
-      - default_ns
-      - merge_code
-      - hail_run_image
-      - build_hail_jar_and_wheel
-  - kind: buildImage2
-    name: netcat_ubuntu_image
-    publishAs: netcat
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
-        FROM $BASE_IMAGE
-        RUN hail-apt-get-install netcat-openbsd
-    dependsOn:
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: volume_image
-    publishAs: volume
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
-        FROM $BASE_IMAGE
-        VOLUME ["/data"]
-        WORKDIR "/tmp"
-        VOLUME ["relative_volume"]
-    dependsOn:
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: gpu_image
-    publishAs: gpu
-    resources:
-      storage: 10Gi
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
-        FROM $BASE_IMAGE
-        RUN hail-pip-install torch torchvision -f https://download.pytorch.org/whl/cu113/torch_stable.html
-    dependsOn:
-      - hail_ubuntu_image
-  - kind: buildImage2
-    name: workdir_image
-    publishAs: workdir
-    dockerFile:
-      inline: |
-        ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
-        FROM $BASE_IMAGE
-        WORKDIR ["/work"]
-    dependsOn:
-      - hail_ubuntu_image
-  - kind: runImage
-    name: test_batch
-    numSplits: 5
-    image:
-      valueFrom: batch_image.image
-    script: |
-      set -ex
-
-      # Use the test identity's credentials instead of CI's
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export HAIL_TEST_GSA_KEY_FILE=/test-gsa-key/key.json
-      export HAIL_TEST_DEV_GSA_KEY_FILE=/test-dev-gsa-key/key.json
-
-      export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
-      export CI_UTILS_IMAGE={{ ci_utils_image.image }}
-      export HAIL_CURL_IMAGE={{ hail_ubuntu_image.image }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
-      export HAIL_VOLUME_IMAGE={{ volume_image.image }}
-      export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
-      export DOCKER_PREFIX="{{ global.docker_prefix }}"
-      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
-      export HAIL_GENETICS_HAILTOP_IMAGE="{{ hailgenetics_hailtop_image.image }}"
-      export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
-      export HAIL_TOKEN="{{ token }}"
-      export HAIL_CLOUD="{{ global.cloud }}"
-      export HAIL_PRODUCTION_DOMAIN="{{ global.domain }}"
-      export HAIL_GPU_IMAGE="{{ gpu_image.image }}"
-      export HAIL_BATCH_REMOTE_TMPDIR="{{ global.test_storage_uri }}/test_batch/{{ token }}/"
-
-      hail-pip-install -r /io/dev-requirements.txt
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --log-date-format="%Y-%m-%dT%H:%M:%S" \
-              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
-              -k "not test_scale and not test_invariants" \
-              --timeout=360 \
-              /io/test/
-    inputs:
-      - from: /repo/batch/test
-        to: /io/test
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/dev-requirements.txt
-    port: 5000
-    timeout: 1500
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    dependsOn:
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - merge_code
-      - deploy_batch
-      - batch_image
-      - ci_utils_image
-      - hailgenetics_hail_image
-      - hailgenetics_hailtop_image
-      - netcat_ubuntu_image
-      - volume_image
-      - workdir_image
-      - hail_ubuntu_image
-      - gpu_image
-  - kind: runImage
-    name: test_auth
-    numSplits: 1
-    image:
-      valueFrom: auth_image.image
-    script: |
-      set -ex
-
-      hail-pip-install -r /io/dev-requirements.txt
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --log-date-format="%Y-%m-%dT%H:%M:%S" \
-              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
-              --timeout=360 \
-              /io/test/
-    inputs:
-      - from: /repo/auth/test
-        to: /io/test
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/dev-requirements.txt
-    timeout: 1500
-    dependsOn:
-      - auth_image
-  - kind: runImage
-    name: delete_test_billing_projects
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: batch_image.image
-    script: |
-      set -ex
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_TEST_DEV_GSA_KEY_FILE=/test-dev-gsa-key/key.json
-      export HAIL_TOKEN="{{ test_batch.token }}"
-      cd /io/test
-      python3 -c '
-      import billing_projects
-      import asyncio
-      asyncio.get_event_loop().run_until_complete(billing_projects.delete_all_test_billing_projects())
-      '
-    inputs:
-      - from: /repo/batch/test
-        to: /io/test
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    alwaysRun: true
-    dependsOn:
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - merge_code
-      - batch_image
-      - deploy_batch
-      - test_batch
-  - kind: runImage
-    name: create_ci_test_repo
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -e
-      TOKEN=$(cat /secret/ci-secrets/user1)
-      REPO_NAME="ci-test-{{token}}"
-
-      echo creating $REPO_NAME...
-      curl -XPOST \
-        -i \
-        -fsSL \
-        https://api.github.com/orgs/hail-ci-test/repos \
-        -H "Authorization: token ${TOKEN}" \
-        -d "{ \"name\" : \"$REPO_NAME\" }"
-
-      # checkout new ci repo
-      # Repeated clones should happen in fresh directories so we mv to the final
-      # destination on successful clone
-      set +x
-      clone() {
-        tmp_dir=$(mktemp -d) && git clone https://$1@github.com/hail-ci-test/$2.git $tmp_dir && mv $tmp_dir $2
-      }
-      typeset -fx clone
-      retry clone $TOKEN $REPO_NAME
-      set -x
-      cd $REPO_NAME
-
-      mkdir -p ./ci/test ./hail/
-      cp /io/repo/ci/test/resources/build.yaml ./
-      cp -R /io/repo/ci/* ./ci/
-      cp /io/repo/tls/Dockerfile ./ci/test/resources/Dockerfile.certs
-      cp /io/repo/tls/create_certs.py ./ci/test/resources/
-      cp /io/repo/tls/create_test_db_config.sh ./ci/test/resources/
-      cp /io/repo/pylintrc ./
-      cp /io/repo/check-sql.sh ./
-      cp /io/repo/pyproject.toml ./
-      cp -R /io/repo/docker ./
-      cp -R /io/repo/gear ./
-      cp -R /io/repo/hail/python ./hail/
-      cp /io/repo/hail/Makefile ./hail/
-      cp /io/repo/hail/env_var.mk ./hail/
-      cp -R /io/repo/web_common ./
-      cp /io/repo/hail/python/setup-hailtop.py ./hail/python/
-
-      git config user.name ci
-      git config user.email ci@hail.is
-      git add * && git commit -m "setup repo"
-      retry git push
-    secrets:
-      - name: hail-ci-0-1-service-account-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /secret/ci-secrets
-    scopes:
-      - test
-      - dev
-    inputs:
-      - from: /repo
-        to: /io/repo
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - merge_code
-  - kind: runImage
-    name: create_ci_config
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      kubectl -n {{ default_ns.name }} create secret generic ci-config \
-          --from-literal=github_context="ci-test" \
-          --from-literal=storage_uri="{{ global.test_storage_uri }}" \
-          --from-literal=deploy_steps="[]" \
-          --from-literal=watched_branches="[[\"hail-ci-test/ci-test-{{create_ci_test_repo.token}}:main\", true, true]]" \
-          --save-config --dry-run=client -o yaml \
-        | kubectl -n {{ default_ns.name }} apply -f -
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - create_ci_test_repo
-  - kind: deploy
-    name: deploy_ci
+    mountPath: /global-config
+  inputs:
+  - from: /repo/ci/bootstrap_create_accounts.py
+    to: /io/bootstrap_create_accounts.py
+  dependsOn:
+  - default_ns
+  - deploy_test_batch_sa
+  - auth_database
+  - auth_image
+  - create_deploy_config
+  - deploy_auth_driver_service_account
+  - create_test_gsa_keys
+  - create_test_database_server_config
+- kind: buildImage2
+  name: hailgenetics_vep_grch37_85_image
+  dockerFile: /io/repo/docker/hailgenetics/vep/grch37/85/Dockerfile
+  contextPath: /io/repo/docker/vep/
+  publishAs: hailgenetics/vep-grch37-85
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - merge_code
+- kind: buildImage2
+  name: hailgenetics_vep_grch38_95_image
+  dockerFile: /io/repo/docker/hailgenetics/vep/grch38/95/Dockerfile
+  contextPath: /io/repo/docker/vep/
+  publishAs: hailgenetics/vep-grch38-95
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - merge_code
+- kind: buildImage2
+  name: monitoring_image
+  dockerFile: /io/repo/monitoring/Dockerfile
+  contextPath: /io/repo
+  publishAs: monitoring
+  inputs:
+  - from: /repo/monitoring
+    to: /io/repo/monitoring
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: buildImage2
+  name: batch_image
+  dockerFile: /io/repo/batch/Dockerfile
+  contextPath: /io/repo
+  publishAs: batch
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/batch
+    to: /io/repo/batch
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: buildImage2
+  name: hailgenetics_hailtop_image
+  dockerFile: /io/repo/docker/hailgenetics/hailtop/Dockerfile
+  contextPath: /io/repo
+  publishAs: hailgenetics/hailtop
+  inputs:
+  - from: /repo/docker/hailgenetics/hailtop
+    to: /io/repo/docker/hailgenetics/hailtop
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  dependsOn:
+  - merge_code
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: ci_image
+  dockerFile: /io/repo/ci/Dockerfile
+  contextPath: /io/repo
+  publishAs: ci
+  inputs:
+  - from: /repo/ci
+    to: /io/repo/ci
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  dependsOn:
+  - hail_ubuntu_image
+  - merge_code
+- kind: buildImage2
+  name: hail_buildkit_image
+  dockerFile: /io/repo/ci/buildkit/Dockerfile
+  contextPath: /io/repo/ci
+  publishAs: hail-buildkit
+  inputs:
+  - from: /repo/ci
+    to: /io/repo/ci
+  dependsOn:
+  - merge_code
+  - copy_third_party_images
+- kind: runImage
+  name: build_hail_jar_and_wheel
+  image:
+    valueFrom: base_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=Release
+    time retry sh mill --no-daemon --version
+
+    # We've encountered the following sporadic error in CI between `mill`
+    # finishing assembling the jar and `Make` copying the jar:
+    #
+    # cp -f out/assembly.dest/out.jar python/hail/backend/hail-all-spark.jar
+    # cp: cannot stat 'out/assembly.dest/out.jar': No such file or directory
+    #
+    # This was likely from running mill in server mode; mill main exits before
+    # the jar has finished being written.
+    time retry make shadowJar
+    if [ ! -f out/hail/2.12/assembly.dest/out.jar ]; then
+        echo 'no out.jar found after mill assembly returned. going to sleep'
+        sleep 5
+    fi
+
+    time retry make DEV_CLARIFIER=hail-ci-build wheel
+
+    # Check wheel size is small enough for pypi (< 200 MiB)
+    BYTES=$(du build/deploy/dist/hail-*-py3-none-any.whl | awk '{print $1}')
+    (( BYTES < 209715200 )) || exit 1
+  inputs:
+  - from: /repo
+    to: /io/repo
+  outputs:
+  - from: /io/repo/hail/out
+    to: /derived/release/hail/out/
+  - from: /io/repo/hail/build/deploy/dist
+    to: /derived/release/hail/build/deploy/dist
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: runImage
+  name: upload_temporary_hailctl_artifacts
+  image:
+    valueFrom: ci_utils_image.image
+  resources:
+    memory: standard
+    cpu: '1'
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
+    make HAIL_BUILD_MODE=Release DEV_CLARIFIER=hail-ci-build upload-artifacts \
+        -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
+  dependsOn:
+  - ci_utils_image
+  - default_ns
+  - merge_code
+  - build_hail_jar_and_wheel
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/hail/build/deploy/dist
+  secrets:
+  - name: test-dataproc-service-account-key
     namespace:
       valueFrom: default_ns.name
-    config: ci/deployment.yaml
-    wait:
-      - kind: Service
-        name: ci
-        for: alive
-    dependsOn:
-      - default_ns
-      - ci_image
-      - ci_utils_image
-      - create_accounts
-      - ci_database
-      - deploy_auth
-      - deploy_batch
-      - create_ci_config
-      - deploy_ci_agent
-      - create_certs
-      - hail_buildkit_image
-  - kind: runImage
-    name: test_ci_unit
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_image.image
-    script: |
-      set -ex
-      hail-pip-install -r /io/dev-requirements.txt
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              /io/ci/unit-test
-    timeout: 1200
-    inputs:
-      - from: /repo/ci
-        to: /io/ci
-      - from: /repo/hail/python/dev/pinned-requirements.txt
-        to: /io/dev-requirements.txt
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - merge_code
-      - ci_image
-  - kind: runImage
-    name: test_ci
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: hail_dev_image.image
-    script: |
-      set -ex
-      export ORGANIZATION=hail-ci-test
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export REPO_NAME=ci-test-"{{ create_ci_test_repo.token }}"
-      export NAMESPACE="{{ default_ns.name }}"
-      pip install /io/ci
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              /io/ci/test
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    timeout: 5400
-    inputs:
-      - from: /repo/ci
-        to: /io/ci
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - merge_code
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - create_certs
-      - deploy_ci
-      - hail_dev_image
-      - create_ci_test_repo
-  - kind: runImage
-    name: test_hailtop_python
-    resources:
-      memory: standard
-      cpu: '0.25'
-    numSplits: 5
-    image:
-      valueFrom: hail_dev_image.image
-    script: |
-      cd /io
-      set -ex
-
-      tar xzf test.tar.gz
-      python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
-
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-
-      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
-      export HAIL_GENETICS_HAILTOP_IMAGE="{{ hailgenetics_hailtop_image.image }}"
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
-
-      {% if global.cloud == 'gcp' %}
-      export GCS_REQUESTER_PAYS_PROJECT={{ global.gcp_project }}
-      {% endif %}
-
-      hailctl config set batch/billing_project test
-      hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/test_hailtop_python/{{ token }}/
-
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --timeout=360 \
-              --ignore=test/hailtop/inter_cloud \
-              test/hailtop
-    inputs:
-      - from: /test.tar.gz
-        to: /io/test.tar.gz
-      - from: /derived/debug/hail/build/deploy/dist
-        to: /io/debug-wheel
-    timeout: 1200
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - hailgenetics_hail_image
-      - hailgenetics_hailtop_image
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - hail_dev_image
-      - hail_debug_wheel
-      - deploy_batch
-  - kind: runImage
-    name: test_hailctl_batch
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: hailgenetics_hail_image.image
-    script: |
-      set -ex
-
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
-
-      {% if global.cloud == "gcp" %}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      {% elif global.cloud == "azure" %}
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      {% else %}
-      echo "unknown cloud {{ global.cloud }}"
-      exit 1
-      {% endif %}
-
-
-      hailctl config set batch/billing_project test
-      hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/hailctl-test/{{ token }}
-
-      mkdir -p foo
-      echo "bar" > foo/baz.txt
-
-      cat >simple_hail.py <<EOF
-      import hail as hl
-
-      with open('foo/baz.txt') as f:
-          print(f.read())
-
-      hl.init(app_name='test-hailctl-batch-submit-query')
-      hl.utils.range_table(10).collect()
-      EOF
-      
-      # https://stackoverflow.com/questions/3524978/logging-functions-in-bash-and-stdout 
-      exec 3>&1
-      
-      function log { echo "$@" 1>&3; }
-      
-      function submit {
-        local status=$(hailctl batch submit --quiet --output json --wait "$@")
-        log "$status"
-        log $(hailctl batch log -o json $(jq -jr '.batch_id' <<< "$status") 1)  # print the job log
-        test $(jq -jr '.state' <<< "$status") = "Success"
-      }
-
-      submit -v simple_hail.py:/ -v foo/:/foo/ --workdir / --name=test-hailctl-batch-submit python3 simple_hail.py
-      
-      cat >hail_with_args.py <<EOF
-      import hail as hl
-      import sys
-
-      with open('foo/baz.txt') as f:
-          print(f.read())
-
-      hl.init(app_name='test-hailctl-batch-submit-query')
-      assert hl.utils.range_table(int(sys.argv[1]))._force_count() == 100
-      EOF
-
-      submit -v hail_with_args.py:/ -v foo/:/foo/ --workdir / --name=test-hailctl-batch-submit python3 hail_with_args.py 100
-      
-      cat >file.sh <<EOF
-      set -ex
-
-      cat foo/baz.txt
-      echo "Hello World!"
-      EOF
-
-      submit --shell /bin/sh --name=test-hailctl-batch-submit -v file.sh:/ -v foo/:/foo/ -o json --image busybox:latest sh file.sh
-      
-      cat >file-with-args.sh <<EOF
-      [ "$#" -eq 2 ]
-
-      cat foo/baz.txt
-      echo "Hello World! $1 $2"
-      EOF
-
-      submit --name=test-hailctl-batch-submit -v file-with-args.sh:/ -v foo/:/foo/ -o json --image ubuntu:latest sh file-with-args.sh abc 123
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - hailgenetics_hail_image
-      - upload_query_jar
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - merge_code
-      - deploy_batch
-  - kind: runImage
-    name: test_batch_docs
-    image:
-      valueFrom: hail_dev_image.image
-    script: |
-      set -ex
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      hailctl config set batch/billing_project test
-      hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/test_batch_docs/{{ token }}/
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --doctest-modules \
-              --doctest-glob='*.rst' \
-              --doctest-continue-on-failure \
-              --ignore=docs/cookbook/files/ \
-              --timeout=120 \
-              --ignore=docs/conf.py \
-              /io/hailtop/batch
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - hail_dev_image
-      - merge_code
-      - deploy_batch
-    timeout: 1200
-    inputs:
-      - from: /repo/hail/python/hailtop
-        to: /io/hailtop
-  - kind: runImage
-    name: cleanup_ci_test_repo
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
+    mountPath: /test-dataproc-service-account-key
+  scopes:
+  - deploy
+  - dev
+  clouds:
+  - gcp
+- kind: runImage
+  name: build_hail_debug_jar_and_wheel
+  image:
+    valueFrom: base_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=CI
+    time retry sh mill --no-daemon --version
+
+    # See `build_hail_jar_and_wheel`
+    time retry make shadowJar
+    if [ ! -f out/hail/2.12/assembly.dest/out.jar ]; then
+        echo 'no out.jar found after mill assembly returned. going to sleep'
+        sleep 5
+    fi
+
+    time retry make wheel
+  inputs:
+  - from: /repo
+    to: /io/repo
+  outputs:
+  - from: /io/repo/hail/out
+    to: /derived/debug/hail/out
+  - from: /io/repo/hail/build/deploy/dist
+    to: /derived/debug/hail/build/deploy/dist
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: runImage
+  name: build_debug_hail_test_jar
+  image:
+    valueFrom: base_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    export MILLOPTS='--no-daemon' HAIL_BUILD_MODE=CI
+    time retry sh mill --no-daemon --version
+
+    # See `build_hail_jar_and_wheel`
+    time retry make shadowTestJar
+    if [ ! -f out/hail/2.12/test/assembly.dest/out.jar ]; then
+        echo 'no out.jar found after mill assembly returned. going to sleep'
+        sleep 5
+    fi
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/debug/hail/out
+    to: /io/repo/hail/out
+  outputs:
+  - from: /io/repo/hail/out
+    to: /derived/debug/hail/out
+  dependsOn:
+  - base_image
+  - merge_code
+  - build_hail_debug_jar_and_wheel
+- kind: runImage
+  name: build_hail_test_artifacts
+  image:
+    valueFrom: base_image.image
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    time tar czf test.tar.gz -C python test pytest.ini
+    time tar czf resources.tar.gz -C hail/test resources
+    time tar czf data.tar.gz -C python/hail/docs data
+    time TESTNG_SPLITS=5 python3 generate_splits.py
+    time tar czf splits.tar.gz testng-splits-*.xml
+  inputs:
+  - from: /repo
+    to: /io/repo
+  outputs:
+  - from: /io/repo/hail/test.tar.gz
+    to: /test.tar.gz
+  - from: /io/repo/hail/resources.tar.gz
+    to: /resources.tar.gz
+  - from: /io/repo/hail/splits.tar.gz
+    to: /splits.tar.gz
+  - from: /io/repo/hail/data.tar.gz
+    to: /data.tar.gz
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: buildImage2
+  name: hail_run_image
+  dockerFile: /io/repo/hail/Dockerfile.hail-run
+  contextPath: /io/repo
+  publishAs: hail-run
+  resources:
+    storage: 10Gi
+    cpu: "2"
+    memory: standard
+  inputs:
+  - from: /repo/hail/Dockerfile.hail-run
+    to: /io/repo/hail/Dockerfile.hail-run
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/repo/hail/python/dev/pinned-requirements.txt
+  - from: /repo/docker/core-site.xml
+    to: /io/repo/docker/core-site.xml
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: runImage
+  name: jvm_entryway_jar
+  image:
+    valueFrom: base_image.image
+  script: |
+    set -ex
+
+    cd /io/batch/jvm-entryway
+    time retry sh mill --no-daemon --version
+    sh mill --no-daemon assembly
+  inputs:
+  - from: /repo/batch
+    to: /io/batch
+  outputs:
+  - from: /io/batch/jvm-entryway/out/assembly.dest/out.jar
+    to: /jvm-entryway.jar
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: buildImage2
+  name: batch_worker_image
+  dockerFile: /io/repo/batch/Dockerfile.worker
+  contextPath: /io/repo
+  publishAs: batch-worker
+  inputs:
+  - from: /repo/letsencrypt/subdomains.txt
+    to: /io/repo/letsencrypt/subdomains.txt
+  - from: /repo/docker
+    to: /io/repo/docker
+  - from: /repo/batch
+    to: /io/repo/batch
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  - from: /jvm-entryway.jar
+    to: /io/repo/batch/jvm-entryway/out/assembly.dest/out.jar
+  dependsOn:
+  - merge_code
+  - hail_ubuntu_image
+  - jvm_entryway_jar
+- kind: runImage
+  name: upload_test_resources_to_blob_storage
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+    cd /io/repo/hail/
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    python3 -m hailtop.aiotools.copy 'null' '[
+    {"from": "hail/test/resources",
+     "to":   "{{ global.test_storage_uri }}/{{ token }}/test/resources"},
+    {"from": "python/hail/docs/data",
+     "to":   "{{ global.test_storage_uri }}/{{ token }}/doctest/data"}
+    ]'
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  inputs:
+  - from: /repo/hail/hail/test/resources
+    to: /io/repo/hail/hail/test/resources
+  - from: /repo/hail/python/hail/docs/data
+    to: /io/repo/hail/python/hail/docs/data
+  dependsOn:
+  - default_ns
+  - hailgenetics_hailtop_image
+  - create_test_gsa_keys
+  - merge_code
+- kind: runImage
+  name: test_hail_java
+  numSplits: 5
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    mkdir -p hail/test
+    tar xzf resources.tar.gz -C hail/test
+    tar xzf splits.tar.gz
+    export HAIL_TEST_SKIP_R=1
+    java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-splits-$HAIL_RUN_IMAGE_SPLIT_INDEX.xml
+  inputs:
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
+    to: /io/hail-test.jar
+  - from: /splits.tar.gz
+    to: /io/splits.tar.gz
+  outputs:
+  - from: /io/test-output
+    to: /test-output
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - hail_run_image
+  - create_test_gsa_keys
+  - build_debug_hail_test_jar
+  - build_hail_test_artifacts
+- kind: runImage
+  name: test_hail_python
+  numSplits: 28
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    tar xzf test.tar.gz
+    tar xzf resources.tar.gz
+    tar xzf data.tar.gz
+    python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
+
+    # pyspark/conf/core-site.xml already points at /gsa-key/key.json
+    mv /test-gsa-key/key.json /gsa-key/key.json
+
+    export HAIL_QUERY_N_CORES=2
+    export OMP_NUM_THREADS=2
+    export OPENBLAS_NUM_THREADS=2
+    export MKL_NUM_THREADS=2
+    export VECLIB_MAXIMUM_THREADS=2
+    export NUMEXPR_NUM_THREADS=2
+
+    export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
+    export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
+    export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
+    export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
+
+    python3 -m pytest \
+            -Werror:::hail -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --timeout=120 \
+            test/hail
+  inputs:
+  - from: /derived/debug/hail/build/deploy/dist
+    to: /io/debug-wheel
+  - from: /test.tar.gz
+    to: /io/test.tar.gz
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /data.tar.gz
+    to: /io/data.tar.gz
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - hail_run_image
+  - create_test_gsa_keys
+  - build_hail_debug_jar_and_wheel
+  - build_hail_test_artifacts
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_hailtop_python_fs
+  numSplits: 5
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    tar xzf test.tar.gz
+
+    python3 -m pip install -r test-requirements.txt
+
+    export HAIL_TEST_GCS_BUCKET={{ global.hail_test_gcs_bucket }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+
+    export HAIL_TEST_S3_BUCKET=hail-test-dy5rg
+    export AWS_SHARED_CREDENTIALS_FILE=/test-aws-key/credentials
+
+    export HAIL_TEST_AZURE_ACCOUNT=hailtest
+    export HAIL_TEST_AZURE_CONTAINER=hail-test-4nxei
+    # Required for SAS testing on Azure
+    export HAIL_TEST_AZURE_RESGRP=hail-dev
+    export HAIL_TEST_AZURE_SUBID=22cd45fe-f996-4c51-af67-ef329d977519
+    export AZURE_APPLICATION_CREDENTIALS=/test-azure-key/credentials.json
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --timeout=120 \
+            test/hailtop/inter_cloud
+  timeout: 1200
+  inputs:
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/test-requirements.txt
+  - from: /test.tar.gz
+    to: /io/test.tar.gz
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  - name: test-aws-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-aws-key
+  - name: test-azure-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-azure-key
+  dependsOn:
+  - default_ns
+  - hailgenetics_hailtop_image
+  - create_test_gsa_keys
+  - build_hail_test_artifacts
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_hail_python_unchecked_allocator
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    tar xzf test.tar.gz
+    tar xzf resources.tar.gz
+    tar xzf data.tar.gz
+    python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
+
+    # pyspark/conf/core-site.xml already points at /gsa-key/key.json
+    mv /test-gsa-key/key.json /gsa-key/key.json
+
+    export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
+    export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
+    export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
+    export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            -m unchecked_allocator \
+            --ignore=test/hailtop/batch/ \
+            --ignore=test/hailtop/inter_cloud \
+            --timeout=120 \
+            test
+  inputs:
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  - from: /test.tar.gz
+    to: /io/test.tar.gz
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /data.tar.gz
+    to: /io/data.tar.gz
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - hail_run_image
+  - build_hail_jar_and_wheel
+  - build_hail_test_artifacts
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_hail_python_local_backend
+  numSplits: 48
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    tar xzf test.tar.gz
+    tar xzf resources.tar.gz
+    tar xzf data.tar.gz
+    python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
+    mkdir -p /io/tmp
+
+    # The test should use the test credentials, not CI's credentials
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+
+    export HAIL_QUERY_N_CORES=2
+    export OMP_NUM_THREADS=2
+    export OPENBLAS_NUM_THREADS=2
+    export MKL_NUM_THREADS=2
+    export VECLIB_MAXIMUM_THREADS=2
+    export NUMEXPR_NUM_THREADS=2
+
+    export HAIL_CLOUD={{ global.cloud }}
+    export HAIL_TEST_STORAGE_URI=/io/tmp/
+    export HAIL_TEST_RESOURCES_DIR=$(realpath ./resources)
+    export HAIL_DOCTEST_DATA_DIR=$(realpath ./data)
+    export HAIL_LOCAL_BACKEND_HEAP_SIZE=3G
+
+    hailctl config set query/backend local
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --ignore=test/hailtop/ \
+            --timeout=120 \
+            test
+  timeout: 1800
+  inputs:
+  - from: /derived/debug/hail/build/deploy/dist
+    to: /io/debug-wheel
+  - from: /test.tar.gz
+    to: /io/test.tar.gz
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /data.tar.gz
+    to: /io/data.tar.gz
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - hail_run_image
+  - create_test_gsa_keys
+  - build_hail_debug_jar_and_wheel
+  - build_hail_test_artifacts
+- kind: runImage
+  name: test_python_docs
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
+
+    export HAIL_QUERY_N_CORES=2
+    export OMP_NUM_THREADS=2
+    export OPENBLAS_NUM_THREADS=2
+    export MKL_NUM_THREADS=2
+    export VECLIB_MAXIMUM_THREADS=2
+    export NUMEXPR_NUM_THREADS=2
+
+    export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
+    export HAIL_LOCATION=$(dirname $(python3 -c 'import hail; print(hail.__file__)'))
+
+    mv /io/docs $HAIL_LOCATION/docs
+
+    # NB: do not use --timeout with doctest because there is no way to override it.
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --doctest-modules \
+            --doctest-glob='*.rst' \
+            --doctest-continue-on-failure \
+            --ignore=$HAIL_LOCATION/test \
+            --ignore=$HAIL_LOCATION/docs/conf.py \
+            --ignore=$HAIL_LOCATION/docs/doctest_write_data.py \
+            --rootdir $HAIL_LOCATION \
+            $HAIL_LOCATION
+  inputs:
+  - from: /repo/hail/python/hail/docs
+    to: /io/docs
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  dependsOn:
+  - build_hail_jar_and_wheel
+  - hail_run_image
+  clouds:
+  - gcp
+- kind: runImage
+  name: make_docs
+  resources:
+    memory: standard
+    cpu: '4'
+  image:
+    valueFrom: hail_run_image.image
+  script: |
+    set -ex
+    set -o pipefail
+    export HAIL_USE_PRIVATE_LENS_DATA=1
+    export HAIL_SHORT_VERSION='0.2'
+    export SPHINXOPTS='-tgenerate_notebook_outputs'
+
+    python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
+
+    cd /io/hail
+    export HAIL_WEBSITE_DIR=/io/website/website/
+
+    sed -E "s/\(hail\#([0-9]+)\)/(\[#\1](https:\/\/github.com\/hail-is\/hail\/pull\/\1))/g" \
+      < python/hail/docs/change_log.md \
+      | pandoc -o python/hail/docs/change_log.rst --fail-if-warnings --verbose
+
+    make -C python/hail/docs BUILDDIR=_build clean html
+    make -C python/hailtop/batch/docs BUILDDIR=_build clean html
+
+    mkdir -p www/docs
+    mv python/hail/docs/_build/html www/docs/0.2
+    mv python/hailtop/batch/docs/_build/html www/docs/batch
+
+    HAIL_CACHE_VERSION=$(cat env/HAIL_VERSION)
+    find www -iname *.html -type f -exec sed -i -e "s/\.css/\.css\?v\=$HAIL_CACHE_VERSION/" {} +;
+
+    tar czf /io/www.tar.gz www
+  inputs:
+  - from: /repo/hail
+    to: /io/hail
+  - from: /repo/website/website
+    to: /io/website/website
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  outputs:
+  - from: /io/www.tar.gz
+    to: /www.tar.gz
+  dependsOn:
+  - merge_code
+  - build_hail_jar_and_wheel
+  - hail_run_image
+- kind: buildImage2
+  name: hailgenetics_hail_image
+  dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
+  contextPath: /io/repo
+  publishAs: hailgenetics/hail
+  buildArgs:
+  - name: BASE_IMAGE
+    value:
       valueFrom: hail_ubuntu_image.image
-    script: |
-      set -e
-      TOKEN=$(cat /secret/ci-secrets/user1)
-      echo deleting ci-test-{{ create_ci_test_repo.token }}...
-      curl -XDELETE \
-        -ifsSL \
-        https://api.github.com/repos/hail-ci-test/ci-test-{{ create_ci_test_repo.token }} \
-        -H "Authorization: token ${TOKEN}"
-    secrets:
-      - name: hail-ci-0-1-service-account-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /secret/ci-secrets
-    alwaysRun: true
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - default_ns
-      - hail_ubuntu_image
-      - create_ci_test_repo
-      - deploy_ci
-      - test_ci
-  - kind: runImage
-    name: test_dataproc-37
-    image:
-      valueFrom: ci_utils_image.image
-    resources:
-      preemptible: False
-    script: |
-      set -ex
-
-      cd /io/repo
-
-      gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
-      gcloud config set project hail-vdc
-      gcloud config set dataproc/region us-central1
-
-      if git ls-remote --exit-code --tags origin $(cat hail/env/HAIL_PIP_VERSION)
-      then
-          echo "tag $HAIL_PIP_VERSION already exists"
-          exit 0
-      fi
-
-      cd hail
-      make test-dataproc-37 HAIL_BUILD_MODE=Release \
-          -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
-    dependsOn:
-      - ci_utils_image
-      - default_ns
-      - merge_code
-      - upload_temporary_hailctl_artifacts
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/hail/build/deploy/dist
-    secrets:
-      - name: test-dataproc-service-account-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dataproc-service-account-key
-    scopes:
-      - deploy
-      - dev
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_dataproc-38
-    image:
-      valueFrom: ci_utils_image.image
-    resources:
-      preemptible: False
-    script: |
-      set -ex
-
-      cd /io/repo
-
-      gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
-      gcloud config set project hail-vdc
-      gcloud config set dataproc/region us-central1
-
-      if git ls-remote --exit-code --tags origin $(cat hail/env/HAIL_PIP_VERSION)
-      then
-          echo "tag $HAIL_PIP_VERSION already exists"
-          exit 0
-      fi
-
-      cd hail
-      make test-dataproc-38 HAIL_BUILD_MODE=Release \
-          -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
-    dependsOn:
-      - ci_utils_image
-      - default_ns
-      - merge_code
-      - upload_temporary_hailctl_artifacts
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/repo/hail/build/deploy/dist
-    scopes:
-      - deploy
-      - dev
-    clouds:
-      - gcp
-  - kind: runImage
-    name: release
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      cd /io
-
-      gcloud auth activate-service-account --key-file=/ci-deploy-0-1--hail-is-hail/ci-deploy-0-1--hail-is-hail.json
-
-      gcloud auth -q configure-docker {{ global.docker_prefix.split('/')[0] }}
-      cat /docker-hub-hailgenetics/password | skopeo login --username hailgenetics --password-stdin docker.io
-
-      cp /pypi-credentials/pypirc $HOME/.pypirc
-      printf 'Authorization: token ' > github-oauth
-      cat /hail-ci-0-1-github-oauth-token/oauth-token >>github-oauth
-      printf '#!/bin/bash\necho ' > git-askpass
-      cat /hail-ci-0-1-github-oauth-token/oauth-token >>git-askpass
-      chmod 755 git-askpass
-      export GIT_ASKPASS=/io/git-askpass
-
-      cd /io/repo/hail
-      export HAIL_PIP_VERSION=$(cat env/HAIL_PIP_VERSION)
-
-      if git ls-remote --exit-code --tags origin $HAIL_PIP_VERSION
-      then
-          echo "tag $HAIL_PIP_VERSION already exists"
-          echo '0' > /io/release-hail-flag
-          exit 0
-      fi
-
-      # #14452 - must build wheel with release `hailtop/hailctl/deploy.yaml`
-      # use `-o` to prevent `mill` from rebuilding the "SHADOW_JAR"
-      make upload-artifacts HAIL_BUILD_MODE=Release DEPLOY_REMOTE=origin \
-        -o out/hail/2.12/assembly.dest/out.jar
-
-      echo Setting arguments and invoking release.sh.
-
-      HAIL_VERSION=$(cat env/HAIL_VERSION) \
-      WHEEL="build/deploy/dist/hail-${HAIL_PIP_VERSION}-py3-none-any.whl" \
-      GIT_VERSION=$(cat env/REVISION) \
-      REMOTE=origin \
-      GITHUB_OAUTH_HEADER_FILE=/io/github-oauth \
-      HAIL_GENETICS_HAIL_IMAGE=docker://{{ hailgenetics_hail_image.image }} \
-      HAIL_GENETICS_HAIL_IMAGE_PY_3_10=docker://{{ hailgenetics_hail_image_python_3_10.image }} \
-      HAIL_GENETICS_HAIL_IMAGE_PY_3_11=docker://{{ hailgenetics_hail_image.image }} \
-      HAIL_GENETICS_HAIL_IMAGE_PY_3_12=docker://{{ hailgenetics_hail_image_python_3_12.image }} \
-      HAIL_GENETICS_HAIL_IMAGE_PY_3_13=docker://{{ hailgenetics_hail_image_python_3_13.image }} \
-      HAIL_GENETICS_HAILTOP_IMAGE=docker://{{ hailgenetics_hailtop_image.image }} \
-      HAIL_GENETICS_VEP_GRCH37_85_IMAGE=docker://{{ hailgenetics_vep_grch37_85_image.image }} \
-      HAIL_GENETICS_VEP_GRCH38_95_IMAGE=docker://{{ hailgenetics_vep_grch38_95_image.image }} \
-      AZURE_WHEEL=/io/azure-wheel/hail-*-py3-none-any.whl \
-      WEBSITE_TAR=/io/www.tar.gz \
-      bash scripts/release.sh
-
-      echo '1' > /io/release-hail-flag
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/release/hail/out/hail/2.12/assembly.dest/out.jar
-        to: /io/repo/hail/out/hail/2.12/assembly.dest/out.jar
-      - from: /azure-wheel
-        to: /io/azure-wheel
-      - from: /www.tar.gz
-        to: /io/www.tar.gz
-    outputs:
-      - from: /io/release-hail-flag
-        to: /release-hail-flag
-    secrets:
-      - name: pypi-credentials
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /pypi-credentials
-      - name: ci-deploy-0-1--hail-is-hail
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /ci-deploy-0-1--hail-is-hail
-      - name: docker-hub-hailgenetics
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /docker-hub-hailgenetics
-      - name: hail-ci-0-1-github-oauth-token
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /hail-ci-0-1-github-oauth-token
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - merge_code
-      - hailgenetics_hail_image
-      - hailgenetics_hail_image_python_3_10
-      - hailgenetics_hail_image_python_3_12
-      - hailgenetics_hail_image_python_3_13
-      - hailgenetics_hailtop_image
-      - hailgenetics_vep_grch37_85_image
-      - hailgenetics_vep_grch38_95_image
-      - build_hail_jar_and_wheel
-      - build_azure_wheel
-      - test_hail_java
-      - test_hail_python
-      - test_hailtop_python
-      - test_hail_python_local_backend
-      - test_hail_python_service_backend_gcp
-      - test_hail_python_service_backend_azure
-      - test_hail_scala_fs
-      - test_hail_services_java
-      - test_hail_spark_conf_requester_pays_parsing
-      - test_dataproc-37
-      - test_dataproc-38
-      - make_docs
-    clouds:
-      - gcp
-  - kind: runImage
-    name: deploy_wheel
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      gcloud auth activate-service-account --key-file=/gsa-key/key.json
-      HAIL_WHEEL_FILE=hail-$(cat /io/repo/hail/env/HAIL_PIP_VERSION)-py3-none-any.whl
-      gcloud storage cp "/io/wheel/$HAIL_WHEEL_FILE" "gs://cpg-hail-ci/wheels/$HAIL_WHEEL_FILE"
-    inputs:
-      - from: /repo
-        to: /io/repo
-      - from: /derived/release/hail/build/deploy/dist
-        to: /io/wheel
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - build_hail_jar_and_wheel
-    clouds:
-      - gcp
-  - kind: runImage
-    name: deploy_hailgenetics_image
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      gcloud auth -q configure-docker australia-southeast1-docker.pkg.dev
-      skopeo copy docker://{{ hailgenetics_hail_image.image }} docker://australia-southeast1-docker.pkg.dev/hail-295901/hail/hailgenetics/hail:$(cat /io/repo/hail/env/HAIL_PIP_VERSION)
-      skopeo copy docker://{{ hailgenetics_hailtop_image.image }} docker://australia-southeast1-docker.pkg.dev/hail-295901/hail/hailgenetics/hailtop:$(cat /io/repo/hail/env/HAIL_PIP_VERSION)
-    inputs:
-      - from: /repo
-        to: /io/repo
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - hailgenetics_hail_image
-      - hailgenetics_hailtop_image
-    clouds:
-      - gcp
-  - kind: runImage
-    name: make_terra_prs
-    image:
-      valueFrom: ci_utils_image.image
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - release
-    inputs:
-      - from: /release-hail-flag
-        to: /io/release-hail-flag
-      - from: /repo
-        to: /io/repo
-    secrets:
-      - name: hail-ci-0-1-github-oauth-token
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /hail-ci-0-1-github-oauth-token
-    clouds:
-      - gcp
-    scopes:
-      - deploy
-      - dev
-    script: |
-      set -ex
-      if [[ $(< /io/release-hail-flag) != '1' ]]
-      then
-          echo 'Skipping making terra update prs (no new release published)'
-          exit 0
-      fi
-
-      printf 'Authorization: token ' > github-oauth
-      cat /hail-ci-0-1-github-oauth-token/oauth-token >> /io/github-oauth
-      printf '#!/bin/bash\necho ' > git-askpass
-      cat /hail-ci-0-1-github-oauth-token/oauth-token >> /io/git-askpass
-      chmod 755 /io/git-askpass
-      export GIT_ASKPASS=/io/git-askpass
-
-      cd /io/repo/hail
-      export HAIL_PIP_VERSION=$(cat env/HAIL_PIP_VERSION)
-      export GITHUB_OAUTH_HEADER_FILE=/io/github-oauth
-      bash scripts/make-terra-prs.sh
-  - kind: runImage
-    name: mirror_hailgenetics_images
-    image: quay.io/skopeo/stable:v1.13.2
-    script: |
-      set -ex
-
-      REGISTRY={{ global.docker_prefix.split('/')[0] }}
-
-      set +x
-      {% if global.cloud == "gcp" %}
-      cat $GOOGLE_APPLICATION_CREDENTIALS | base64 -w 0 | skopeo login -u _json_key_base64 --password-stdin $REGISTRY
-      {% elif global.cloud == "azure" %}
-      dnf install -y jq
-      USERNAME=$(cat $AZURE_APPLICATION_CREDENTIALS | jq -jr '.appId')
-      cat $AZURE_APPLICATION_CREDENTIALS | jq -jr '.password' | skopeo login -u $USERNAME --password-stdin $REGISTRY
-      {% else %}
-      echo "unknown cloud {{ global.cloud }}"
-      exit 1
-      {% endif %}
-      set -x
-
-      cd /io/docker/hailgenetics
-      export HAIL_PIP_VERSION=$(cat /io/HAIL_PIP_VERSION)
-      export DOCKER_PREFIX={{ global.docker_prefix }}
-      bash mirror_images.sh
-    inputs:
-      - from: /repo/hail/env/HAIL_PIP_VERSION
-        to: /io/HAIL_PIP_VERSION
-      - from: /repo/docker/hailgenetics/mirror_images.sh
-        to: /io/docker/hailgenetics/mirror_images.sh
-      - from: /repo/docker/copy_image.sh
-        to: /io/docker/copy_image.sh
-    scopes:
-      - deploy
-      - dev
-    dependsOn:
-      - default_ns
-      - merge_code
-  - kind: buildImage2
-    name: website_image
-    dockerFile: /io/repo/website/Dockerfile
-    contextPath: /io/repo
-    publishAs: website
-    inputs:
-      - from: /repo/website
-        to: /io/repo/website
-      - from: /docs.tar.gz
-        to: /io/repo/docs.tar.gz
-      - from: /repo/hail/python/setup-hailtop.py
-        to: /io/repo/hail/python/setup-hailtop.py
-      - from: /repo/hail/python/MANIFEST.in
-        to: /io/repo/hail/python/MANIFEST.in
-      - from: /repo/hail/python/hailtop
-        to: /io/repo/hail/python/hailtop
-      - from: /repo/gear
-        to: /io/repo/gear
-      - from: /repo/web_common
-        to: /io/repo/web_common
-    dependsOn:
-      - hail_ubuntu_image
-      - get_pip_versioned_docs
-    clouds:
-      - gcp
-    resources:
-      storage: 20Gi
-      cpu: "2"
-      memory: standard
-  - kind: deploy
-    name: deploy_website
+  - name: HAIL_WHEEL_DIR
+    value: /wheel
+  inputs:
+  - from: /repo/docker/hailgenetics/hail
+    to: /io/repo/docker/hailgenetics/hail
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/wheel
+  dependsOn:
+  - merge_code
+  - build_hail_jar_and_wheel
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: hailgenetics_hail_image_python_3_10
+  dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
+  contextPath: /io/repo
+  publishAs: hailgenetics/hail
+  buildArgs:
+  - name: BASE_IMAGE
+    value:
+      valueFrom: hail_ubuntu_image_python_3_10.image
+  - name: HAIL_WHEEL_DIR
+    value: /wheel
+  inputs:
+  - from: /repo/docker/hailgenetics/hail
+    to: /io/repo/docker/hailgenetics/hail
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/wheel
+  dependsOn:
+  - merge_code
+  - build_hail_jar_and_wheel
+  - hail_ubuntu_image_python_3_10
+- kind: buildImage2
+  name: hailgenetics_hail_image_python_3_12
+  dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
+  contextPath: /io/repo
+  publishAs: hailgenetics/hail
+  buildArgs:
+  - name: BASE_IMAGE
+    value:
+      valueFrom: hail_ubuntu_image_python_3_12.image
+  - name: HAIL_WHEEL_DIR
+    value: /wheel
+  inputs:
+  - from: /repo/docker/hailgenetics/hail
+    to: /io/repo/docker/hailgenetics/hail
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/wheel
+  dependsOn:
+  - merge_code
+  - build_hail_jar_and_wheel
+  - hail_ubuntu_image_python_3_12
+- kind: buildImage2
+  name: hailgenetics_hail_image_python_3_13
+  dockerFile: /io/repo/docker/hailgenetics/hail/Dockerfile
+  contextPath: /io/repo
+  publishAs: hailgenetics/hail
+  buildArgs:
+  - name: BASE_IMAGE
+    value:
+      valueFrom: hail_ubuntu_image_python_3_13.image
+  - name: HAIL_WHEEL_DIR
+    value: /wheel
+  inputs:
+  - from: /repo/docker/hailgenetics/hail
+    to: /io/repo/docker/hailgenetics/hail
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/wheel
+  dependsOn:
+  - merge_code
+  - build_hail_jar_and_wheel
+  - hail_ubuntu_image_python_3_13
+- kind: runImage
+  name: test_hailgenetics_hail_image
+  image:
+    valueFrom: hailgenetics_hail_image.image
+  script: |
+    set -ex
+    python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 11, sys.version_info'
+    python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
+    python3 -c 'import numpy; import pandas; import sklearn; import scipy'
+  dependsOn:
+  - hailgenetics_hail_image
+- kind: runImage
+  name: test_hailgenetics_hail_image_python_3_10
+  image:
+    valueFrom: hailgenetics_hail_image_python_3_10.image
+  script: |
+    set -ex
+    python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 10, sys.version_info'
+    python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
+    python3 -c 'import numpy; import pandas; import sklearn; import scipy'
+  dependsOn:
+  - hailgenetics_hail_image_python_3_10
+- kind: runImage
+  name: test_hailgenetics_hail_image_python_3_12
+  image:
+    valueFrom: hailgenetics_hail_image_python_3_12.image
+  script: |
+    set -ex
+    python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 12, sys.version_info'
+    python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
+    python3 -c 'import numpy; import pandas; import sklearn; import scipy'
+  dependsOn:
+  - hailgenetics_hail_image_python_3_12
+- kind: runImage
+  name: test_hailgenetics_hail_image_python_3_13
+  image:
+    valueFrom: hailgenetics_hail_image_python_3_13.image
+  script: |
+    set -ex
+    python3 -c 'import sys; assert sys.version_info.major == 3 and sys.version_info.minor == 13, sys.version_info'
+    python3 -c 'import hail as hl; hl.balding_nichols_model(3, 100, 100)._force_count_rows()'
+    python3 -c 'import numpy; import pandas; import sklearn; import scipy'
+  dependsOn:
+  - hailgenetics_hail_image_python_3_13
+- kind: buildImage2
+  name: hail_dev_image
+  dockerFile: /io/repo/docker/Dockerfile.hail-dev
+  contextPath: /io/repo
+  publishAs: hail-dev
+  inputs:
+  - from: /repo/docker/Dockerfile.hail-dev
+    to: /io/repo/docker/Dockerfile.hail-dev
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/repo/hail/python/dev/pinned-requirements.txt
+  dependsOn:
+  - hailgenetics_hail_image
+  - merge_code
+- kind: buildImage2
+  name: hail_linting_image
+  contextPath: /io/repo
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
+      FROM $BASE_IMAGE
+      RUN hail-apt-get-install git make openjdk-11-jre-headless
+      COPY hail/python/pinned-requirements.txt hail-requirements.txt
+      COPY hail/python/dev/pinned-requirements.txt dev-requirements.txt
+      COPY gear/pinned-requirements.txt gear-requirements.txt
+      COPY web_common/pinned-requirements.txt web_common-requirements.txt
+      COPY batch/pinned-requirements.txt batch-requirements.txt
+      COPY ci/pinned-requirements.txt ci-requirements.txt
+      RUN python3 -m pip install \
+          -r hail-requirements.txt \
+          -r dev-requirements.txt \
+          -r gear-requirements.txt \
+          -r web_common-requirements.txt \
+          -r batch-requirements.txt \
+          -r ci-requirements.txt \
+          && \
+          python3 -m pyright --version # Force the installation of node and npm pyright in the image
+  publishAs: linting
+  inputs:
+  - from: /repo/hail/python/pinned-requirements.txt
+    to: /io/repo/hail/python/pinned-requirements.txt
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/repo/hail/python/dev/pinned-requirements.txt
+  - from: /repo/gear/pinned-requirements.txt
+    to: /io/repo/gear/pinned-requirements.txt
+  - from: /repo/web_common/pinned-requirements.txt
+    to: /io/repo/web_common/pinned-requirements.txt
+  - from: /repo/batch/pinned-requirements.txt
+    to: /io/repo/batch/pinned-requirements.txt
+  - from: /repo/ci/pinned-requirements.txt
+    to: /io/repo/ci/pinned-requirements.txt
+  dependsOn:
+  - merge_code
+  - hail_ubuntu_image
+- kind: runImage
+  name: check_pip_requirements
+  image:
+    valueFrom: hail_linting_image.image
+  script: |
+    set -ex
+    cd /io/repo
+    chmod 755 ./check_pip_requirements.sh
+    make check-pip-requirements
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - hail_linting_image
+  - merge_code
+- kind: runImage
+  name: check_services
+  image:
+    valueFrom: hail_linting_image.image
+  script: |
+    set -ex
+    cd /io/repo
+    {% if 'target_sha' in code %}
+    export HAIL_TARGET_SHA={{ code.target_sha }}
+    {% endif %}
+    make -k check-services
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - hail_linting_image
+  - merge_code
+- kind: runImage
+  name: check_hail
+  image:
+    valueFrom: hail_linting_image.image
+  resources:
+    memory: 8G
+  script: |
+    set -ex
+    cd /io/repo
+    make check-hail
+  inputs:
+  - from: /repo/Makefile
+    to: /io/repo/Makefile
+  - from: /repo/pylintrc
+    to: /io/repo/pylintrc
+  - from: /repo/pyproject.toml
+    to: /io/repo/pyproject.toml
+  - from: /repo/hail
+    to: /io/repo/hail
+  - from: /repo/config.mk
+    to: /io/repo/config.mk
+  dependsOn:
+  - hail_linting_image
+  - merge_code
+- kind: runImage
+  name: compile_hail_213
+  image:
+    valueFrom: base_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io/repo/hail
+
+    HAIL_BUILD_MODE='CI'
+    time retry sh mill --no-daemon hail[2.13].__.compile
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - base_image
+  - merge_code
+- kind: runImage
+  name: get_pip_versioned_docs
+  image:
+    valueFrom: hailgenetics_hail_image.image
+  script: |
+    set -ex
+
+    cd /io/repo
+
+    # dev deploy elides the hail-is remote, add it and retrieve the tags
+    git remote add hail-is https://github.com/hail-is/hail.git
+
+    export HAIL_PIP_VERSION=$(cat hail/env/HAIL_PIP_VERSION)
+
+    if git ls-remote --exit-code --tags hail-is $HAIL_PIP_VERSION
+    then
+      # In this case, we want to get the docs from Google Storage.
+      python3 -m hailtop.aiotools.copy 'null' '[
+      {"from": "gs://hail-common/website/'$HAIL_PIP_VERSION'/www.tar.gz",
+      "to": "www.tar.gz"}
+      ]'
+    else
+      cp /io/www.tar.gz .
+    fi
+
+    mkdir -p hail/build/www/docs/0.2
+    tar -xvf www.tar.gz -C hail/build/www/docs --strip-components 2 --no-same-owner
+
+    python3 -m hailtop.aiotools.copy 'null' '[
+    {"from": "gs://hail-common/builds/0.1/docs/hail-0.1-docs-5a6778710097.tar.gz",
+     "to": "hail-0.1-docs-5a6778710097.tar.gz"}
+    ]'
+
+    mkdir -p hail/build/www/docs/0.1
+    tar -xvf hail-0.1-docs-5a6778710097.tar.gz -C hail/build/www/docs/0.1 --strip-components 2 --no-same-owner
+
+    tar czf /io/docs.tar.gz -C hail/build/www .
+  resources:
+    memory: standard
+    cpu: '2'
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /www.tar.gz
+    to: /io/www.tar.gz
+  outputs:
+  - from: /io/docs.tar.gz
+    to: /docs.tar.gz
+  dependsOn:
+  - hailgenetics_hail_image
+  - merge_code
+  - make_docs
+  clouds:
+  - gcp
+- kind: deploy
+  name: deploy_grafana
+  namespace:
+    valueFrom: default_ns.name
+  config: grafana/deployment.yaml
+  scopes:
+  - deploy
+  - test
+  - dev
+  dependsOn:
+  - default_ns
+  - hail_ubuntu_image
+  - create_certs
+  - copy_third_party_images
+- kind: deploy
+  name: deploy_prometheus
+  namespace:
+    valueFrom: default_ns.name
+  config: prometheus/prometheus.yaml
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - create_certs
+  - copy_third_party_images
+- kind: deploy
+  name: deploy_auth
+  namespace:
+    valueFrom: default_ns.name
+  config: auth/deployment.yaml
+  wait:
+  - kind: Service
+    name: auth
+    for: alive
+  - kind: Service
+    name: auth-driver
+    for: alive
+  dependsOn:
+  - default_ns
+  - create_deploy_config
+  - create_session_key
+  - auth_database
+  - auth_image
+  - create_certs
+  - create_accounts
+- kind: runImage
+  name: create_initial_user
+  runIfRequested: true
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+
+    {% if default_ns.name == "default" %}
+    hailctl auth create-user --developer {{ code.username }} {{ code.login_id }}
+    {% else %}
+    hailctl auth create-user \
+      --developer \
+      --hail-identity {{ code.hail_identity }} \
+      --hail-credentials-secret-name {{ code.username }}-gsa-key \
+      {{ code.username }} {{ code.login_id }}
+    {% endif %}
+  secrets:
+  - name: test-dev-gsa-key
     namespace:
       valueFrom: default_ns.name
-    config: website/deployment.yaml
-    wait:
-      - kind: Service
-        name: www
-        for: alive
-    dependsOn:
-      - default_ns
-      - website_image
-      - create_certs
-      - create_session_key
-      - create_deploy_config
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_website
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      set -ex
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      hailctl curl {{ default_ns.name }} www / \
-              -vvv \
-              -fsSL \
-              --retry 3 \
-              --retry-delay 5
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    dependsOn:
-      - default_ns
-      - create_accounts
-      - hailgenetics_hailtop_image
-      - deploy_website
-    clouds:
-      - gcp
-  - kind: runImage
-    name: test_hail_scala_fs
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-      cd /io
-      mkdir -p src/test
-      tar xzf resources.tar.gz -C src/test
-
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
-      export HAIL_FS_TEST_CLOUD_RESOURCES_URI={{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/test/resources/fs
-      export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}
-
-      set +e
-      java -Xms7500M -Xmx7500M \
-           -cp hail-test.jar:$SPARK_HOME/jars/* \
-           org.testng.TestNG \
-           -listener is.hail.LogTestListener \
-           testng-fs.xml
-      exit_code=$?
-      set -e
-      if [[ $exit_code -eq 2 ]]
-      then
-          echo "some tests were skipped, but exiting success anyway"
-          exit 0
-      else
-          exit $exit_code
-      fi
-    inputs:
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
-        to: /io/hail-test.jar
-      - from: /repo/hail/testng-fs.xml
-        to: /io/testng-fs.xml
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    timeout: 1200
-    dependsOn:
-      - default_ns
-      - create_certs
-      - create_accounts
-      - hail_run_image
-      - build_debug_hail_test_jar
-      - build_hail_test_artifacts
-      - upload_test_resources_to_blob_storage
-  - kind: runImage
-    name: test_hail_services_java
-    image:
-      valueFrom: hail_run_image.image
-    resources:
-      memory: standard
-      cpu: '2'
-    script: |
-      set -ex
-
-      export HAIL_CLOUD={{ global.cloud }}
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-
-      cd /io
-      mkdir -p src/test
-      tar xzf resources.tar.gz -C src/test
-      java -Xms7500M -Xmx7500M \
-           -cp hail-test.jar:$SPARK_HOME/jars/* \
-           org.testng.TestNG \
-           -listener is.hail.LogTestListener \
-           testng-services.xml
-    inputs:
-      - from: /resources.tar.gz
-        to: /io/resources.tar.gz
-      - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
-        to: /io/hail-test.jar
-      - from: /repo/hail/testng-services.xml
-        to: /io/testng-services.xml
-    secrets:
-      - name: test-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-gsa-key
-    timeout: 1200
-    dependsOn:
-      - default_ns
-      - create_certs
-      - create_accounts
-      - hail_run_image
-      - build_debug_hail_test_jar
-      - build_hail_test_artifacts
-      - upload_query_jar
-      - deploy_batch
-  - kind: runImage
-    name: start_hail_benchmark
-    scopes:
-      - deploy
-      - dev
-    clouds:
-      - gcp
-    dependsOn:
-      - default_ns
-      - hail_dev_image
-      - release
-    image:
-      valueFrom: hail_dev_image.image
-    inputs:
-      - from: /repo/hail/python
-        to: /io/repo/hail/python
-      - from: /repo/hail/env
-        to: /io/repo/hail/env
-      - from: /repo/hail/scripts/benchmark_in_batch.py
-        to: /io/repo/hail/scripts/benchmark_in_batch.py
-      - from: /release-hail-flag
-        to: /io/release-hail-flag
-    script: |
-      set -ex
-
-      # only run benchmarks iff we've published a new release
-      if [[ $(< /io/release-hail-flag) != '1' ]]
-      then
-          echo 'Skipping benchmarks (no new release published).'
-          exit 0
-      fi
-
-      pushd /io/repo/hail
-
-      BUCKET=hail-benchmarks-2
-      HAIL_VERSION=$(cat env/HAIL_VERSION)
-      RESULTS_PREFIX="gs://${BUCKET}/{{ scope }}/${HAIL_VERSION}"
-
-      export HAIL_BATCH_REGIONS={{ global.gcp_region }}
-      export HAIL_BATCH_BILLING_PROJECT=benchmark
-      export HAIL_BATCH_REMOTE_TMPDIR={{ ci_storage_uri }}/{{ token }}
-
-      PYTHONPATH="$PWD/python" python3 ./scripts/benchmark_in_batch.py submit \
-          {{ hail_dev_image.image }} \
-          $RESULTS_PREFIX \
-          $HAIL_VERSION
-
-  - kind: runImage
-    name: cancel_all_running_test_batches
-    image:
-      valueFrom: hailgenetics_hailtop_image.image
-    script: |
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-
-      cat >cancel_all_running_test_batches.py <<'EOF'
-      from hailtop.batch_client.aioclient import BatchClient
-      import asyncio
-      import traceback
-
-      async def cancel_all(query):
-          bc = await BatchClient.create('test')
-          async for b in bc.list_batches(query):
-              status = await b.last_known_status()
-              print(status)
-              try:
-                  await b.cancel()
-              except:
-                  traceback.print_exc()
-
-      asyncio.get_event_loop().run_until_complete(cancel_all('user:test running'))
-      EOF
-
-      python3 cancel_all_running_test_batches.py
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    alwaysRun: true
-    timeout: 300
-    dependsOn:
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - hailgenetics_hailtop_image
-      - deploy_batch
-      - test_batch
-      - test_ci
-      - test_hailtop_python
-      - test_hail_python_service_backend_gcp
-      - test_hail_python_service_backend_azure
-      - test_hail_services_java
-      - test_batch_docs
-      - test_hailctl_batch
-  - kind: runImage
-    name: test_batch_invariants
-    image:
-      valueFrom: hail_dev_image.image
-    script: |
-      export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export AZURE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
-      export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
-      export DOCKER_PREFIX="{{ global.docker_prefix }}"
-      export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
-      python3 -m pytest \
-              -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
-              --log-cli-level=INFO \
-              -s \
-              -r A \
-              -vv \
-              --instafail \
-              --durations=50 \
-              --log-date-format="%Y-%m-%dT%H:%M:%S" \
-              --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
-              --timeout=120 \
-              /io/test/test_invariants.py
-    inputs:
-      - from: /repo/batch/test
-        to: /io/test
-    timeout: 300
-    secrets:
-      - name: test-dev-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /test-dev-gsa-key
-    scopes:
-      - test
-      - dev
-    dependsOn:
-      - create_deploy_config
-      - create_accounts
-      - default_ns
-      - merge_code
-      - hail_dev_image
-      - deploy_batch
-      - test_batch
-      - test_ci
-      - test_hailtop_python
-      - test_hail_python_service_backend_gcp
-      - test_hail_python_service_backend_azure
-      - cancel_all_running_test_batches
-  - kind: runImage
-    name: delete_gcp_batch_instances
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    alwaysRun: true
-    script: |
-      set -ex
-      gcloud -q auth activate-service-account --key-file=/batch-gsa-key/key.json
-      set +e
-      kubectl -n {{ default_ns.name }} scale deployment batch-driver --replicas=0
-      gcloud -q compute instances list \
-          --filter 'tags.items=batch2-agent AND labels.namespace={{ default_ns.name }}' \
-          --format="table[no-heading](zone.basename(), name)" \
-          --project {{ global.gcp_project }} \
-        | xargs -P8 -n2 -r sh -c 'gcloud -q compute instances delete --zone "$1" --project {{ global.gcp_project }} "$2" || true' argv0
-      gcloud -q compute disks list \
-          --filter 'labels.batch=1 AND labels.namespace={{ default_ns.name }}' \
-          --format="table[no-heading](zone.basename(), name)" \
-          --project {{ global.gcp_project }} \
-        | xargs -P8 -n2 -r sh -c 'gcloud -q compute disks delete --zone "$1" --project {{ global.gcp_project }} "$2" || true' argv0
-    secrets:
-      - name: batch-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /batch-gsa-key
-    scopes:
-      - dev
-      - test
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    clouds:
-      - gcp
-    dependsOn:
-      - default_ns
-      - ci_utils_image
-      - test_batch_invariants
-      - test_batch
-      - test_ci
-      - test_hailtop_python
-      - test_hail_python_service_backend_gcp
-      - test_hail_python_service_backend_azure
-      - cancel_all_running_test_batches
-  - kind: runImage
-    name: delete_azure_batch_instances
-    image: mcr.microsoft.com/azure-cli:azurelinux3.0
-    alwaysRun: true
-    script: |
-      set -e -o pipefail
-      AZURE_USERNAME=$(jq -r '.appId' /batch-gsa-key/key.json)
-      AZURE_PASSWORD=$(jq -r '.password' /batch-gsa-key/key.json)
-      AZURE_TENANT_ID=$(jq -r '.tenant' /batch-gsa-key/key.json)
-      az login --service-principal -u $AZURE_USERNAME -p $AZURE_PASSWORD --tenant $AZURE_TENANT_ID
-      set +e
-      set -x
-      export AZURE_RESOURCE_GROUP="{{ global.azure_resource_group }}"
-      az aks install-cli
-      kubectl -n {{ default_ns.name }} scale deployment batch-driver --replicas=0
-      az vm list --resource-group $AZURE_RESOURCE_GROUP -o tsv \
-          --query "[?tags.namespace == '{{ default_ns.name }}'].name" \
-        | xargs -n1 -r sh -c 'az vm delete --force-deletion true --resource-group $AZURE_RESOURCE_GROUP --name "$1" --yes || true' argv0
-      az network nic list --resource-group $AZURE_RESOURCE_GROUP -o tsv \
-          --query "[?tags.namespace == '{{ default_ns.name }}'].name" \
-        | xargs -n1 -r sh -c 'az network nic delete --resource-group $AZURE_RESOURCE_GROUP --name "$1" || true' argv0
-      az network public-ip list --resource-group $AZURE_RESOURCE_GROUP -o tsv \
-          --query "[?tags.namespace == '{{ default_ns.name }}'].name" \
-        | xargs -n1 -r sh -c 'az network public-ip delete --resource-group $AZURE_RESOURCE_GROUP --name "$1" || true' argv0
-      az deployment group list --resource-group $AZURE_RESOURCE_GROUP -o tsv \
-          --query "[?tags.namespace == '{{ default_ns.name }}'].name" \
-        | xargs -n1 -r sh -c 'az deployment delete --name "$1" || true' argv0
-    secrets:
-      - name: batch-gsa-key
-        namespace:
-          valueFrom: default_ns.name
-        mountPath: /batch-gsa-key
-    scopes:
-      - dev
-      - test
-    serviceAccount:
-      name: admin
-      namespace:
-        valueFrom: default_ns.name
-    clouds:
-      - azure
-    dependsOn:
-      - default_ns
-      - test_batch_invariants
-      - test_batch
-      - test_ci
-      - test_hailtop_python
-      - test_hail_python_service_backend_gcp
-      - test_hail_python_service_backend_azure
-      - cancel_all_running_test_batches
-  - kind: runImage
-    name: setup_dev_namespace_autoscaledown
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      {% for user in code.get("developers", []) %}
-      {% if user['username'] != 'test-dev' %}
-
-      if kubectl get namespace {{ user["username"] }} 2>/dev/null
-      then
-      cat > the.yaml <<'EOF'
-      apiVersion: batch/v1
-      kind: CronJob
-      metadata:
-        name: dev-namespace-scaledown-{{ user["username"] }}
-        namespace: {{ user["username"] }}
-      spec:
-        schedule: "0 0 * * *"  # Every day at midnight UTC
-        concurrencyPolicy: Forbid
-        successfulJobsHistoryLimit: 1
-        failedJobsHistoryLimit: 1
-        jobTemplate:
-          spec:
-            template:
-              spec:
-                serviceAccountName: admin
-                containers:
-                - name: dev-namespace-scaledown-{{ user["username"] }}
-                  image: bitnami/kubectl:latest
-                  command:
-                  - /bin/sh
-                  - -c
-                  - set -ex ; kubectl scale deployments --all -n {{ user["username"] }} --replicas=0 && kubectl scale statefulsets --all -n {{ user["username"] }} --replicas=0
-                restartPolicy: OnFailure
-      EOF
-
-      kubectl apply -f the.yaml
-      echo "For {{ user["username"] }}, applied:"
-      echo "---"
-      cat the.yaml
-      else
-      echo "Skipping {{ user["username"] }} because they have no namespace."
-      fi
-
-      {% endif %}
-      {% endfor %}
-    scopes:
-      - deploy
-    serviceAccount:
-      name: ci-agent
-      namespace:
-        valueFrom: default_ns.name
-    dependsOn:
-      - ci_utils_image
-      - default_ns
-  - kind: runImage
-    name: test_gcp_ar_cleanup_policies
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    script: |
-      set -ex
-      cd /io/repo/
-      new_policy=$(mktemp)
-      python3 devbin/generate_gcp_ar_cleanup_policy.py > $new_policy
-      diff $new_policy infra/gcp-broad/gcp-ar-cleanup-policy.txt || {
-        echo '>>> AR cleanup policy has changed, new policy is <<<'
-        cat $new_policy
-        echo '--------------------------------------'
-        echo "Please regenerate the policy file by running:"
-        echo "> python3 devbin/generate_gcp_ar_cleanup_policy.py > infra/gcp-broad/gcp-ar-cleanup-policy.txt"
+    mountPath: /test-dev-gsa-key
+  dependsOn:
+  - default_ns
+  - hailgenetics_hailtop_image
+  - merge_code
+  - deploy_auth
+- kind: runImage
+  name: delete_monitoring_tables
+  image:
+    valueFrom: monitoring_image.image
+  script: |
+    set -ex
+    cd /io
+    python3 delete_dev_database.py {{ default_ns.name }} monitoring
+  inputs:
+  - from: /repo/ci/delete_dev_database.py
+    to: /io/delete_dev_database.py
+  secrets:
+  - name: database-server-config
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /sql-config
+  serviceAccount:
+    name: admin
+    namespace:
+      valueFrom: default_ns.name
+  network: private
+  runIfRequested: true
+  scopes:
+  - dev
+  dependsOn:
+  - default_ns
+  - monitoring_image
+  - merge_code
+  - create_test_database_server_config
+- kind: createDatabase2
+  name: monitoring_database
+  databaseName: monitoring
+  image:
+    valueFrom: ci_utils_image.image
+  migrations:
+  - name: initial
+    script: /io/sql/000-initial.sql
+  inputs:
+  - from: /repo/monitoring/sql
+    to: /io/sql
+  namespace:
+    valueFrom: default_ns.name
+  shutdowns:
+  - kind: Deployment
+    namespace:
+      valueFrom: default_ns.name
+    name: monitoring
+  dependsOn:
+  - default_ns
+  - merge_code
+  - delete_monitoring_tables
+  - ci_utils_image
+  - create_test_database_server_config
+  - deploy_test_db
+- kind: deploy
+  name: deploy_monitoring
+  namespace:
+    valueFrom: default_ns.name
+  config: monitoring/deployment.yaml
+  wait:
+  - kind: Service
+    name: monitoring
+    for: alive
+  dependsOn:
+  - default_ns
+  - monitoring_image
+  - monitoring_database
+  - deploy_auth
+  - create_certs
+  - create_accounts
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_monitoring
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hail_dev_image.image
+  script: |
+    set -ex
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --timeout=120 \
+            /io/monitoring/test
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  timeout: 300
+  inputs:
+  - from: /repo/monitoring/test
+    to: /io/monitoring/test
+  dependsOn:
+  - hail_dev_image
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - create_certs
+  - deploy_monitoring
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_auth_copy_paste_login
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+
+    # Or else hailctl will try to authenticate as CI
+    unset HAIL_IDENTITY_PROVIDER_JSON
+
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json
+
+    COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
+                       auth /api/v1alpha/copy-paste-token \
+                       -fsSL \
+                       --retry 10 \
+                       --retry-delay 5 \
+                       -XPOST)
+    hailctl auth copy-paste-login "$COPY_PASTE_TOKEN"
+
+    if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN"
+    then
+        echo "reusing a token should not work, but did"
         exit 1
-      }
-    inputs:
-      - from: /repo/build.yaml
-        to: /io/repo/build.yaml
-      - from: /repo/devbin
-        to: /io/repo/devbin
-      - from: /repo/infra
-        to: /io/repo/infra
-      - from: /repo/docker
-        to: /io/repo/docker
-      - from: /repo/ci/test/resources
-        to: /io/repo/ci/test/resources
-    clouds:
-      - gcp
-    dependsOn:
-      - ci_utils_image
-      - default_ns
-  - kind: runImage
-    name: set_gcp_ar_cleanup_policies
-    resources:
-      memory: standard
-      cpu: '0.25'
-    image:
-      valueFrom: ci_utils_image.image
-    scopes:
-      - deploy
-    script: |
-      gcloud artifacts repositories set-cleanup-policies hail \
-        --project={{ global.gcp_project }} \
-        --location=us \
-        --policy=/io/repo/infra/gcp-broad/gcp-ar-cleanup-policy.txt \
-        --no-dry-run
-    inputs:
-      - from: /repo/infra
-        to: /io/repo/infra
-    clouds:
-      - gcp
-    dependsOn:
-      - test_gcp_ar_cleanup_policies
-      - ci_utils_image
+    fi
+
+    COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
+                       auth /api/v1alpha/copy-paste-token \
+                       -fsSL \
+                       --retry 3 \
+                       --retry-delay 5 \
+                       -XPOST)
+    python3 -c '
+    from hailtop.auth import copy_paste_login;
+    copy_paste_login("'$COPY_PASTE_TOKEN'")
+    '
+
+    python3 -c '
+    from hailtop.auth import copy_paste_login;
+    import aiohttp
+    try:
+        copy_paste_login("'$COPY_PASTE_TOKEN'")
+        print("reusing a token should not work, but did")
+        sys.exit(1)
+    except aiohttp.client_exceptions.ClientResponseError as exc:
+        assert(exc.status == 401)
+    '
+  secrets:
+  - name: test-tokens
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /user-tokens
+  dependsOn:
+  - default_ns
+  - create_accounts
+  - deploy_auth
+  - create_deploy_config
+  - hailgenetics_hailtop_image
+- kind: runImage
+  name: test_auth_copy_paste_login_timeout
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+
+    # Or else hailctl will try to authenticate as CI
+    unset HAIL_IDENTITY_PROVIDER_JSON
+
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json
+
+    COPY_PASTE_TOKEN=$(hailctl curl {{ default_ns.name }} \
+                       auth /api/v1alpha/copy-paste-token \
+                       -fsSL \
+                       --retry 10 \
+                       --retry-delay 5 \
+                       -XPOST)
+    sleep $(( 5 * 60 + 1))
+    if hailctl auth copy-paste-login "$COPY_PASTE_TOKEN" --namespace {{ default_ns.name }}
+    then
+        echo "using an expired token should not work, but did"
+        exit 1
+    fi
+
+    python3 -c '
+    import aiohttp
+    from hailtop.auth import copy_paste_login;
+    try:
+        copy_paste_login("'$COPY_PASTE_TOKEN'")
+        print("using an expired token should not work, but did")
+        sys.exit(1)
+    except aiohttp.client_exceptions.ClientResponseError as exc:
+        assert(exc.status == 401)
+    '
+  secrets:
+  - name: test-tokens
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /user-tokens
+  dependsOn:
+  - default_ns
+  - create_accounts
+  - deploy_auth
+  - create_deploy_config
+  - hailgenetics_hailtop_image
+- kind: runImage
+  name: delete_batch_tables
+  image:
+    valueFrom: batch_image.image
+  script: |
+    set -ex
+    cd /io
+    python3 delete_dev_database.py {{ default_ns.name }} batch
+  inputs:
+  - from: /repo/ci/delete_dev_database.py
+    to: /io/delete_dev_database.py
+  secrets:
+  - name: database-server-config
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /sql-config
+  serviceAccount:
+    name: admin
+    namespace:
+      valueFrom: default_ns.name
+  network: private
+  runIfRequested: true
+  scopes:
+  - dev
+  dependsOn:
+  - default_ns
+  - batch_image
+  - merge_code
+  - create_test_database_server_config
+- kind: runImage
+  name: delete_ci_tables
+  image:
+    valueFrom: ci_image.image
+  script: |
+    set -ex
+    cd /io
+    python3 delete_dev_database.py {{ default_ns.name }} ci
+  inputs:
+  - from: /repo/ci/delete_dev_database.py
+    to: /io/delete_dev_database.py
+  secrets:
+  - name: database-server-config
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /sql-config
+  serviceAccount:
+    name: admin
+    namespace:
+      valueFrom: default_ns.name
+  network: private
+  runIfRequested: true
+  scopes:
+  - dev
+  dependsOn:
+  - default_ns
+  - ci_image
+  - merge_code
+  - create_test_database_server_config
+- kind: createDatabase2
+  name: ci_database
+  databaseName: ci
+  image:
+    valueFrom: ci_utils_image.image
+  migrations:
+  - name: initial
+    script: /io/sql/000-initial.sql
+  - name: invalidated-batches
+    script: /io/sql/001-invalidated-batches.sql
+  - name: add-frozen-mode
+    script: /io/sql/002-add-frozen-mode.sql
+    online: true
+  - name: active-namespaces
+    script: /io/sql/003-active-namespaces.sql
+    online: true
+  - name: fix-default-namespace-record
+    script: /io/sql/004-fix-default-namespace.py
+    online: true
+  - name: record-failure-notifications
+    script: /io/sql/005-record-failure-notifications.sql
+    online: true
+  - name: add-service-rate-limits
+    script: /io/sql/006-add-service-rate-limits.sql
+    online: true
+  inputs:
+  - from: /repo/ci/sql
+    to: /io/sql
+  namespace:
+    valueFrom: default_ns.name
+  shutdowns:
+  - kind: Deployment
+    namespace:
+      valueFrom: default_ns.name
+    name: ci
+  dependsOn:
+  - default_ns
+  - merge_code
+  - delete_ci_tables
+  - ci_utils_image
+  - create_test_database_server_config
+  - deploy_test_db
+- kind: createDatabase2
+  name: batch_database
+  databaseName: batch
+  image:
+    valueFrom: ci_utils_image.image
+  migrations:
+  - name: initial
+    script: /io/sql/000-initial.sql
+  - name: insert-globals
+    script: /io/sql/001-insert_globals.py
+  - name: create-billing-projects
+    script: /io/sql/002-create-billing-projects.sql
+  - name: increase-spec-size
+    script: /io/sql/003-increase-spec-size.sql
+  - name: remove-fk-batches-user-resources
+    script: /io/sql/004-remove-fk-batches-user-resources.sql
+  - name: change-ready-cores-bigint
+    script: /io/sql/005-change-ready-cores-bigint.sql
+  - name: add-user-resources-ready-cores-token
+    script: /io/sql/006-add-user-resources-ready-cores-token.sql
+  - name: add-lock-in-share-mode
+    script: /io/sql/007-add-lock-in-share-mode.sql
+  - name: add-batch-create-token
+    script: /io/sql/008-add-batch-create-token.sql
+  - name: improve-cancel
+    script: /io/sql/009-improve-cancel.sql
+  - name: store-specs-in-gcs
+    script: /io/sql/010-store-specs-in-gcs.sql
+  - name: add-batches-time-closed
+    script: /io/sql/011-add-batches-time-closed.sql
+  - name: add-instance-zone
+    script: /io/sql/012-add-instance-zone.sql
+  - name: add-batches-time-created-index
+    script: /io/sql/013-add-batches-time-created-index.sql
+  - name: change-test-worker-disk-size
+    script: /io/sql/014-change_test_worker_disk_size.py
+  - name: add-resources
+    script: /io/sql/015-add-resources.sql
+  - name: insert-resources
+    script: /io/sql/016-insert_resources.py
+  - name: insert-standing-worker-globals
+    script: /io/sql/017-insert_standing_worker_globals.py
+  - name: insert-local-ssd-resource
+    script: /io/sql/018-insert_local_ssd_resource.py
+  - name: fix-mark-job-complete-on-error
+    script: /io/sql/019-fix-mark-job-complete-on-error.sql
+  - name: add-worker-pd-ssd-data-disk
+    script: /io/sql/020-add-worker-pd-ssd-data-disk.sql
+  - name: add-aggregated-batch-resources-tokens
+    script: /io/sql/021-add-aggregated-batch-resources-tokens.sql
+  - name: change-test-worker-pool-size
+    script: /io/sql/022-change_test_worker_pool_size.py
+  - name: add-test-dev-to-billing-project-users
+    script: /io/sql/023-add-test-dev-to-billing-project-users.sql
+  - name: add-status-flag-billing-projects
+    script: /io/sql/024-add-status-flag-billing-projects.sql
+  - name: add-aggregated-billing-project-resources
+    script: /io/sql/025-add-aggregated-billing-project-resources.sql
+  - name: add-enable-standing-worker
+    script: /io/sql/026-add-enable-standing-worker.py
+  - name: add-inst-colls
+    script: /io/sql/027-add-inst-colls.sql
+  - name: add-creating-job-state
+    script: /io/sql/028-add-creating-job-state.sql
+  - name: add-job-private-inst-coll
+    script: /io/sql/029-add-job-private-inst-coll.sql
+  - name: insert-nonpreemptible-resources
+    script: /io/sql/030-insert_nonpreemptible_resources.py
+  - name: fix-schedule-job
+    script: /io/sql/031-fix-schedule-job.sql
+  - name: increase-test-and-dev-pool-sizes
+    script: /io/sql/032-increase-test-and-dev-pool-sizes.py
+  - name: fix-provisioning-bug
+    script: /io/sql/033-fix-provisioning-bug.sql
+  - name: do-not-lock-entire-batch
+    script: /io/sql/034-do-not-lock-entire-batch.sql
+  - name: add-fail-fast
+    script: /io/sql/035-add-fail-fast.sql
+  - name: add-frozen-mode
+    script: /io/sql/036-add-frozen-mode.sql
+  - name: add-instance-config
+    script: /io/sql/037-add-instance-config.sql
+  - name: cloud-agnostic
+    script: /io/sql/038-cloud-agnostic.sql
+  - name: support-azure
+    script: /io/sql/039-support-azure.sql
+  - name: add-azure-tables
+    script: /io/sql/040-add_azure_tables.py
+  - name: change-azure-test-highcpu-pool
+    script: /io/sql/041-change_azure_test_highcpu_pool.py
+  - name: add-latest-product-versions
+    script: /io/sql/042-add-latest-product-versions.sql
+  - name: add-products-and-versions
+    script: /io/sql/043-add_products_and_versions.py
+  - name: kill-more-deadlocks
+    script: /io/sql/044-kill-more-deadlocks.sql
+  - name: kill-more-deadlocks2
+    script: /io/sql/045-kill-more-deadlocks2.sql
+  - name: no-locks-add-attempt
+    script: /io/sql/046-no-locks-add-attempt.sql
+  - name: fix-n-cancelled-creating-jobs
+    script: /io/sql/047-fix-n-cancelled-creating-jobs.sql
+  - name: big-test-instances
+    script: /io/sql/048-big-test-instances.py
+  - name: kill-mjc-deadlocks
+    script: /io/sql/049-kill-mjc-deadlocks.sql
+  - name: add-nonpreemptible-pools
+    script: /io/sql/050-add-nonpreemptible-pools.sql
+  - name: add-pool-label
+    script: /io/sql/050a-add-pool-label.sql
+  - name: set-test-and-dev-pools-to-8-core-max-2
+    script: /io/sql/051-set-test-and-dev-pools-to-8-core-max-2.py
+  - name: set-test-and-dev-jpim-to-max-5
+    script: /io/sql/052-set-test-and-dev-jpim-to-max-5.py
+    online: true
+  - name: minimize-deadlock-errors
+    script: /io/sql/053-minimize-deadlock-errors.sql
+    online: true
+  - name: add-resource-ids-sql
+    script: /io/sql/054-add-resource-ids.sql
+    online: true
+  - name: add-resource-ids-python
+    script: /io/sql/055-add_resource_ids.py
+    online: true
+  - name: modify-resource-id-trigger
+    script: /io/sql/056-modify-resource-id-trigger.sql
+    online: true
+  - name: rm-resource-names-agg-resources
+    script: /io/sql/057-rm-resource-names-agg-resources.sql
+    online: true
+  - name: rm-resource-foreign-keys
+    script: /io/sql/058-rm-resource-foreign-keys.py
+    online: true
+  - name: rm-resource-names-agg-resources-pt-2
+    script: /io/sql/059-rm-resource-names-agg-resources-pt-2.sql
+    online: true
+  - name: add-att-resources-format-version-lt-3
+    script: /io/sql/060-add-att-resources-format-version-lt-3.sql
+    online: true
+  - name: insert-attempt-resources-format-version-lt-3
+    script: /io/sql/061-insert_attempt_resources_format_version_lt_3.py
+    online: true
+  - name: revert-attempt-resources-trigger-back-compat
+    script: /io/sql/062-revert-attempt-resources-trigger-back-compat.sql
+    online: true
+  - name: add-agg-billing-by-date
+    script: /io/sql/063-add-agg-billing-by-date.sql
+    online: true
+  - name: populate-agg-billing-by-date
+    script: /io/sql/064-populate_agg_billing_by_date.py
+    online: true
+  - name: revert-temp-agg-by-date-infra
+    script: /io/sql/065-revert-temp-agg-by-date-infra.sql
+    online: true
+  - name: rename-timestamp-to-date
+    script: /io/sql/066-rename-timestamp-to-date.sql
+    online: true
+  - name: add-real-time-billing
+    script: /io/sql/067-add-real-time-billing.sql
+    online: true
+  - name: add-batch-updates
+    script: /io/sql/068-add-batch-updates.sql
+    online: true
+  - name: populate-batch-updates
+    script: /io/sql/069-populate_batch_updates.py
+    online: true
+  - name: cleanup-add-batch-updates
+    script: /io/sql/070-cleanup-add-batch-updates.sql
+    online: true
+  - name: add-jobs-update-id-index
+    script: /io/sql/071-add-jobs-update-id-index.sql
+    online: true
+  - name: no-dev-standing-workers-by-default
+    script: /io/sql/072-no_dev_standing_workers_by_default.py
+    online: true
+  - name: add-commit-updates
+    script: /io/sql/073-add-commit-updates.sql
+    online: true
+  - name: add-job-regions
+    script: /io/sql/074-add-job-regions.sql
+    online: true
+  - name: faster-regions-pool-scheduler
+    script: /io/sql/075-faster-regions-pool-scheduler.sql
+    online: true
+  - name: add-batch-state-index
+    script: /io/sql/076-add-batch-state-index.sql
+    online: true
+  - name: case-sensitive-billing-project
+    script: /io/sql/077-case-sensitive-billing-project.sql
+    online: true
+  - name: driver-behavior
+    script: /io/sql/078-driver_behavior.py
+    online: true
+  - name: cleanup-old-billing-tables
+    script: /io/sql/079-cleanup-old-billing-tables.sql
+    online: true
+  - name: add-deduped-resource-ids-to-resources
+    script: /io/sql/080-add-deduped-resource-ids-to-resources.sql
+    online: true
+  - name: create-resource-dedup-mapping
+    script: /io/sql/081-create_resource_dedup_mapping.py
+    online: true
+  - name: config-pool-min-instances
+    script: /io/sql/082-config-pool-min-instances.sql
+    online: true
+  - name: add-deduped-resource-ids-to-attempt-resources
+    script: /io/sql/083-add-deduped-resource-ids-to-attempt-resources.sql
+    online: true
+  - name: setup-deduped-resources-migration
+    script: /io/sql/084-setup-deduped-resources-migration.sql
+    online: true
+  - name: dedup-attempt-resources
+    script: /io/sql/085-dedup_attempt_resources.py
+    online: true
+  - name: mitigate-bad-attempt-resources-trigger
+    script: /io/sql/086-mitigate-bad-attempt-resources-trigger.sql
+    online: true
+  - name: set-test-and-dev-pools-to-16-core-max-3
+    script: /io/sql/087-set-test-and-dev-pools-to-16-core-max-3.py
+    online: true
+  - name: fix-billing-triggers-deduped-resource-id
+    script: /io/sql/088-fix-billing-triggers-deduped-resource-id.sql
+    online: true
+  - name: set-test-and-dev-pools-to-max-16-standing-16
+    script: /io/sql/089-set-test-and-dev-pools-to-max-16-standing-16.py
+    online: true
+  - name: set-test-min-pool-size-to-1
+    script: /io/sql/090-set-test-min-pool-size-to-1.py
+    online: true
+  - name: dedup-billing-project-users-v2
+    script: /io/sql/091-dedup_billing_project_users_v2.py
+    online: true
+  - name: list-jobs-extra-indices
+    script: /io/sql/092-list-jobs-extra-indices.sql
+    online: true
+  - name: dedup-billing-project-users-by-date
+    script: /io/sql/093-dedup_billing_project_users_by_date.py
+    online: true
+  - name: add-jobs-ready-time
+    script: /io/sql/094-add-jobs-ready-time.sql
+    online: true
+  - name: add-list-batches-index
+    script: /io/sql/095-add-list-batches-index.sql
+    online: true
+  - name: add-feature-flags
+    script: /io/sql/096-add-feature-flags.sql
+    online: true
+  - name: add-oms-agent-flag
+    script: /io/sql/097-add-oms-agent-flag.sql
+    online: true
+  - name: increase-test-max-idle-time
+    script: /io/sql/098-increase_test_max_idle_time.py
+    online: true
+  - name: turn_off_oms_agent_test_dev
+    script: /io/sql/099-turn_off_oms_agent_test_dev.py
+    online: true
+  - name: add-billing-index-token
+    script: /io/sql/100-add-billing-index-token.sql
+    online: true
+  - name: jobs-after-update-simple.sql
+    script: /io/sql/101-jobs-after-update-simple.sql
+    online: true
+  - name: turn-on-billing-compaction
+    script: /io/sql/102-turn_on_billing_compaction.py
+    online: true
+  - name: cleanup-deprecated-functions
+    script: /io/sql/103-cleanup-deprecated-functions.sql
+    online: true
+  - name: set-test-pools-to-known-parameters
+    script: /io/sql/104-set-test-pools-to-known-parameters.py
+    online: true
+  - name: add-gcp-support-logs-specs-and-firewall-fees
+    script: /io/sql/105-add-gcp-support-logs-specs-and-firewall-fees.py
+    online: true
+  - name: add-product-sku
+    script: /io/sql/106-add-product-sku.sql
+    online: true
+  - name: dedup-agg-batch-resources
+    script: /io/sql/107-dedup_agg_batch_resources.py
+    online: true
+  - name: setup-job-groups
+    script: /io/sql/108-setup-job-groups.sql
+    online: true
+  - name: dedup-job-resources
+    script: /io/sql/109-dedup_job_resources.py
+    online: true
+  - name: fix-job-groups-state-enum
+    script: /io/sql/110-fix-job-groups-state-enum.sql
+    online: true
+  - name: populate-job-groups
+    script: /io/sql/111-populate_job_groups.py
+    online: true
+  - name: rename-job-groups-tables
+    script: /io/sql/112-rename-job-groups-tables.sql
+    online: false # this must be offline
+  - name: remove-v2-billing-writes
+    script: /io/sql/113-remove-v2-billing-writes.sql
+    online: true
+  - name: update-ip-fee-resource
+    script: /io/sql/114-update-ip-fee-resource.py
+    online: true
+  - name: remove-v2-billing-tables
+    script: /io/sql/115-remove-v2-billing-tables.sql
+    online: true
+  - name: finalize-job-groups
+    script: /io/sql/116-finalize-job-groups.sql
+    online: true
+  - name: fix-mark-job-complete-deadlocks
+    script: /io/sql/117-fix-mark-job-complete-deadlocks.sql
+    online: true
+  - name: jobs-add-n-max-attempts
+    script: /io/sql/118-jobs-add-n-max-attempts.sql
+    online: true
+  - name: is-job-cancelled
+    script: /io/sql/119-is-job-cancelled.sql
+    online: true
+  - name: add-dockerhub-proxy-flag
+    script: /io/sql/120-add-dockerhub-proxy-flag.sql
+    online: true
+  inputs:
+  - from: /repo/batch/sql
+    to: /io/sql
+  namespace:
+    valueFrom: default_ns.name
+  shutdowns:
+  - kind: Deployment
+    namespace:
+      valueFrom: default_ns.name
+    name: batch
+  - kind: Deployment
+    namespace:
+      valueFrom: default_ns.name
+    name: batch-driver
+  dependsOn:
+  - default_ns
+  - merge_code
+  - delete_batch_tables
+  - ci_utils_image
+  - create_test_database_server_config
+  - deploy_test_db
+- kind: deploy
+  name: deploy_batch
+  namespace:
+    valueFrom: default_ns.name
+  config: batch/deployment.yaml
+  wait:
+  - kind: Service
+    name: batch
+    for: alive
+  - kind: Service
+    name: batch-driver
+    for: alive
+  dependsOn:
+  - default_ns
+  - deploy_batch_sa
+  - create_accounts
+  - batch_image
+  - batch_worker_image
+  - batch_database
+  - deploy_auth
+  - create_certs
+- kind: runImage
+  name: add_developers
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    {% for user in code.get("developers", []) %}
+    {% if user['username'] != 'test-dev' %}
+    hailctl auth create-user \
+      --developer \
+      --hail-identity {{ user["hail_identity"] }} \
+      --hail-credentials-secret-name {{ user["username"] }}-gsa-key \
+      {{ user["username"] }} {{ user["login_id"] }}
+    {% endif %}
+    {% endfor %}
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  scopes:
+  - dev
+  - test
+  dependsOn:
+  - default_ns
+  - hailgenetics_hailtop_image
+  - deploy_batch
+- kind: runImage
+  name: upload_query_jar
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+    export GOOGLE_APPLICATION_CREDENTIALS=/batch-gsa-key/key.json
+
+    {% if deploy %}
+    HAIL_QUERY_JAR_URL={{ global.query_storage_uri }}
+    {% else %}
+    HAIL_QUERY_JAR_URL={{ global.test_storage_uri }}/{{ default_ns.name }}
+    {% endif %}
+    HAIL_QUERY_JAR_URL=${HAIL_QUERY_JAR_URL}/jars/$(cat /io/REVISION).jar
+
+    python3 -m hailtop.aiotools.copy 'null' '[{"from": "/io/hail.jar", "to": "'${HAIL_QUERY_JAR_URL}'"}]'
+  secrets:
+  - name: batch-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /batch-gsa-key
+  inputs:
+  - from: /derived/release/hail/out/hail/2.12/assembly.dest/out.jar
+    to: /io/hail.jar
+  - from: /repo/hail/env/REVISION
+    to: /io/REVISION
+  dependsOn:
+  - default_ns
+  - deploy_batch
+  - hailgenetics_hailtop_image
+  - build_hail_jar_and_wheel
+  - merge_code
+  - create_test_gsa_keys
+- kind: runImage
+  name: test_hail_python_service_backend_gcp
+  numSplits: 16
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    cpu: '0.25'
+    preemptible: False
+  script: |
+    set -ex
+    python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
+
+    cd /io/repo/hail/python
+
+    export HAIL_CLOUD={{ global.cloud }}
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
+    export HAIL_TEST_RESOURCES_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/test/resources/"
+    export HAIL_DOCTEST_DATA_DIR="{{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/doctest/data/"
+    export HAIL_GENETICS_VEP_GRCH37_85_IMAGE={{ hailgenetics_vep_grch37_85_image.image }}
+    export HAIL_GENETICS_VEP_GRCH38_95_IMAGE={{ hailgenetics_vep_grch38_95_image.image }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+
+    export GCS_REQUESTER_PAYS_PROJECT=broad-ctsa
+
+    export HAIL_SHUFFLE_MAX_BRANCH=4
+    export HAIL_SHUFFLE_CUTOFF=1000000
+    export HAIL_QUERY_BACKEND=batch
+    export HAIL_BATCH_REGIONS={{ global.gcp_region }}
+    export HAIL_BATCH_BILLING_PROJECT=test
+    export HAIL_BATCH_REMOTE_TMPDIR={{ global.test_storage_uri }}
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --ignore=test/hailtop/ \
+            --ignore=test/hail/matrixtable/test_file_formats.py \
+            -m backend \
+            --timeout=600 \
+            test
+  timeout: 5400
+  inputs:
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  - from: /repo/hail/python/pytest.ini
+    to: /io/repo/hail/python/pytest.ini
+  - from: /repo/hail/python/test
+    to: /io/repo/hail/python/test
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - merge_code
+  - deploy_batch
+  - create_deploy_config
+  - create_accounts
+  - hail_run_image
+  - upload_query_jar
+  - upload_test_resources_to_blob_storage
+  - build_hail_jar_and_wheel
+  - hailgenetics_vep_grch37_85_image
+  - hailgenetics_vep_grch38_95_image
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_hail_spark_conf_requester_pays_parsing
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    cpu: '0.5'
+    preemptible: False
+  script: |
+    set -ex
+    python3 -m pip install --no-dependencies /io/wheel/hail-*-py3-none-any.whl
+
+    export YOU_MAY_OVERWRITE_MY_SPARK_DEFAULTS_CONF_AND_HAILCTL_SETTINGS=1
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            /io/test_requester_pays_parsing.py
+  inputs:
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  - from: /repo/hail/scripts/test_requester_pays_parsing.py
+    to: /io/test_requester_pays_parsing.py
+  dependsOn:
+  - default_ns
+  - merge_code
+  - hail_run_image
+  - build_hail_jar_and_wheel
+- kind: buildImage2
+  name: netcat_ubuntu_image
+  publishAs: netcat
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
+      FROM $BASE_IMAGE
+      RUN hail-apt-get-install netcat-openbsd
+  dependsOn:
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: volume_image
+  publishAs: volume
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
+      FROM $BASE_IMAGE
+      VOLUME ["/data"]
+      WORKDIR "/tmp"
+      VOLUME ["relative_volume"]
+  dependsOn:
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: gpu_image
+  publishAs: gpu
+  resources:
+    storage: 10Gi
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
+      FROM $BASE_IMAGE
+      RUN hail-pip-install torch torchvision -f https://download.pytorch.org/whl/cu113/torch_stable.html
+  dependsOn:
+  - hail_ubuntu_image
+- kind: buildImage2
+  name: workdir_image
+  publishAs: workdir
+  dockerFile:
+    inline: |
+      ARG BASE_IMAGE={{ hail_ubuntu_image.image }}
+      FROM $BASE_IMAGE
+      WORKDIR ["/work"]
+  dependsOn:
+  - hail_ubuntu_image
+- kind: runImage
+  name: test_batch
+  numSplits: 5
+  image:
+    valueFrom: batch_image.image
+  script: |
+    set -ex
+
+    # Use the test identity's credentials instead of CI's
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+
+    export HAIL_TEST_GSA_KEY_FILE=/test-gsa-key/key.json
+    export HAIL_TEST_DEV_GSA_KEY_FILE=/test-dev-gsa-key/key.json
+
+    export HAIL_GSA_KEY_FILE=/test-gsa-key/key.json
+    export CI_UTILS_IMAGE={{ ci_utils_image.image }}
+    export HAIL_CURL_IMAGE={{ hail_ubuntu_image.image }}
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_NETCAT_UBUNTU_IMAGE={{ netcat_ubuntu_image.image }}
+    export HAIL_VOLUME_IMAGE={{ volume_image.image }}
+    export HAIL_WORKDIR_IMAGE={{ workdir_image.image }}
+    export DOCKER_PREFIX="{{ global.docker_prefix }}"
+    export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
+    export HAIL_GENETICS_HAILTOP_IMAGE="{{ hailgenetics_hailtop_image.image }}"
+    export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
+    export HAIL_TOKEN="{{ token }}"
+    export HAIL_CLOUD="{{ global.cloud }}"
+    export HAIL_PRODUCTION_DOMAIN="{{ global.domain }}"
+    export HAIL_GPU_IMAGE="{{ gpu_image.image }}"
+    export HAIL_BATCH_REMOTE_TMPDIR="{{ global.test_storage_uri }}/test_batch/{{ token }}/"
+
+    hail-pip-install -r /io/dev-requirements.txt
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --log-date-format="%Y-%m-%dT%H:%M:%S" \
+            --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
+            -k "not test_scale and not test_invariants" \
+            --timeout=360 \
+            /io/test/
+  inputs:
+  - from: /repo/batch/test
+    to: /io/test
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/dev-requirements.txt
+  port: 5000
+  timeout: 1500
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  dependsOn:
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - merge_code
+  - deploy_batch
+  - batch_image
+  - ci_utils_image
+  - hailgenetics_hail_image
+  - hailgenetics_hailtop_image
+  - netcat_ubuntu_image
+  - volume_image
+  - workdir_image
+  - hail_ubuntu_image
+  - gpu_image
+- kind: runImage
+  name: test_auth
+  numSplits: 1
+  image:
+    valueFrom: auth_image.image
+  script: |
+    set -ex
+
+    hail-pip-install -r /io/dev-requirements.txt
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --log-date-format="%Y-%m-%dT%H:%M:%S" \
+            --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
+            --timeout=360 \
+            /io/test/
+  inputs:
+  - from: /repo/auth/test
+    to: /io/test
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/dev-requirements.txt
+  timeout: 1500
+  dependsOn:
+  - auth_image
+- kind: runImage
+  name: delete_test_billing_projects
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: batch_image.image
+  script: |
+    set -ex
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_TEST_DEV_GSA_KEY_FILE=/test-dev-gsa-key/key.json
+    export HAIL_TOKEN="{{ test_batch.token }}"
+    cd /io/test
+    python3 -c '
+    import billing_projects
+    import asyncio
+    asyncio.get_event_loop().run_until_complete(billing_projects.delete_all_test_billing_projects())
+    '
+  inputs:
+  - from: /repo/batch/test
+    to: /io/test
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  alwaysRun: true
+  dependsOn:
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - merge_code
+  - batch_image
+  - deploy_batch
+  - test_batch
+- kind: runImage
+  name: create_ci_test_repo
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -e
+    TOKEN=$(cat /secret/ci-secrets/user1)
+    REPO_NAME="ci-test-{{token}}"
+
+    echo creating $REPO_NAME...
+    curl -XPOST \
+      -i \
+      -fsSL \
+      https://api.github.com/orgs/hail-ci-test/repos \
+      -H "Authorization: token ${TOKEN}" \
+      -d "{ \"name\" : \"$REPO_NAME\" }"
+
+    # checkout new ci repo
+    # Repeated clones should happen in fresh directories so we mv to the final
+    # destination on successful clone
+    set +x
+    clone() {
+      tmp_dir=$(mktemp -d) && git clone https://$1@github.com/hail-ci-test/$2.git $tmp_dir && mv $tmp_dir $2
+    }
+    typeset -fx clone
+    retry clone $TOKEN $REPO_NAME
+    set -x
+    cd $REPO_NAME
+
+    mkdir -p ./ci/test ./hail/
+    cp /io/repo/ci/test/resources/build.yaml ./
+    cp -R /io/repo/ci/* ./ci/
+    cp /io/repo/tls/Dockerfile ./ci/test/resources/Dockerfile.certs
+    cp /io/repo/tls/create_certs.py ./ci/test/resources/
+    cp /io/repo/tls/create_test_db_config.sh ./ci/test/resources/
+    cp /io/repo/pylintrc ./
+    cp /io/repo/check-sql.sh ./
+    cp /io/repo/pyproject.toml ./
+    cp -R /io/repo/docker ./
+    cp -R /io/repo/gear ./
+    cp -R /io/repo/hail/python ./hail/
+    cp /io/repo/hail/Makefile ./hail/
+    cp /io/repo/hail/env_var.mk ./hail/
+    cp -R /io/repo/web_common ./
+    cp /io/repo/hail/python/setup-hailtop.py ./hail/python/
+
+    git config user.name ci
+    git config user.email ci@hail.is
+    git add * && git commit -m "setup repo"
+    retry git push
+  secrets:
+  - name: hail-ci-0-1-service-account-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /secret/ci-secrets
+  scopes:
+  - test
+  - dev
+  inputs:
+  - from: /repo
+    to: /io/repo
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - merge_code
+- kind: runImage
+  name: create_ci_config
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    kubectl -n {{ default_ns.name }} create secret generic ci-config \
+        --from-literal=github_context="ci-test" \
+        --from-literal=storage_uri="{{ global.test_storage_uri }}" \
+        --from-literal=deploy_steps="[]" \
+        --from-literal=watched_branches="[[\"hail-ci-test/ci-test-{{create_ci_test_repo.token}}:main\", true, true]]" \
+        --save-config --dry-run=client -o yaml \
+      | kubectl -n {{ default_ns.name }} apply -f -
+  serviceAccount:
+    name: admin
+    namespace:
+      valueFrom: default_ns.name
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - create_ci_test_repo
+- kind: deploy
+  name: deploy_ci
+  namespace:
+    valueFrom: default_ns.name
+  config: ci/deployment.yaml
+  wait:
+  - kind: Service
+    name: ci
+    for: alive
+  dependsOn:
+  - default_ns
+  - ci_image
+  - ci_utils_image
+  - create_accounts
+  - ci_database
+  - deploy_auth
+  - deploy_batch
+  - create_ci_config
+  - deploy_ci_agent
+  - create_certs
+  - hail_buildkit_image
+- kind: runImage
+  name: test_ci_unit
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_image.image
+  script: |
+    set -ex
+    hail-pip-install -r /io/dev-requirements.txt
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            /io/ci/unit-test
+  timeout: 1200
+  inputs:
+  - from: /repo/ci
+    to: /io/ci
+  - from: /repo/hail/python/dev/pinned-requirements.txt
+    to: /io/dev-requirements.txt
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - merge_code
+  - ci_image
+- kind: runImage
+  name: test_ci
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hail_dev_image.image
+  script: |
+    set -ex
+    export ORGANIZATION=hail-ci-test
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export REPO_NAME=ci-test-"{{ create_ci_test_repo.token }}"
+    export NAMESPACE="{{ default_ns.name }}"
+    pip install /io/ci
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            /io/ci/test
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  timeout: 5400
+  inputs:
+  - from: /repo/ci
+    to: /io/ci
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - merge_code
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - create_certs
+  - deploy_ci
+  - hail_dev_image
+  - create_ci_test_repo
+- kind: runImage
+  name: test_hailtop_python
+  resources:
+    memory: standard
+    cpu: '0.25'
+  numSplits: 5
+  image:
+    valueFrom: hail_dev_image.image
+  script: |
+    cd /io
+    set -ex
+
+    tar xzf test.tar.gz
+    python3 -m pip install --no-dependencies /io/debug-wheel/hail-*-py3-none-any.whl
+
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+
+    export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
+    export HAIL_CLOUD={{ global.cloud }}
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
+    export HAIL_GENETICS_HAILTOP_IMAGE="{{ hailgenetics_hailtop_image.image }}"
+    export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}/{{ token }}
+
+    {% if global.cloud == 'gcp' %}
+    export GCS_REQUESTER_PAYS_PROJECT={{ global.gcp_project }}
+    {% endif %}
+
+    hailctl config set batch/billing_project test
+    hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/test_hailtop_python/{{ token }}/
+
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --timeout=360 \
+            --ignore=test/hailtop/inter_cloud \
+            test/hailtop
+  inputs:
+  - from: /test.tar.gz
+    to: /io/test.tar.gz
+  - from: /derived/debug/hail/build/deploy/dist
+    to: /io/debug-wheel
+  timeout: 1200
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - hailgenetics_hail_image
+  - hailgenetics_hailtop_image
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - hail_dev_image
+  - hail_debug_wheel
+  - deploy_batch
+- kind: runImage
+  name: test_hailctl_batch
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hailgenetics_hail_image.image
+  script: |
+    set -ex
+
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export HAIL_GENETICS_HAIL_IMAGE="{{ hailgenetics_hail_image.image }}"
+
+    {% if global.cloud == "gcp" %}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    {% else %}
+    echo "unknown cloud {{ global.cloud }}"
+    exit 1
+    {% endif %}
+
+
+    hailctl config set batch/billing_project test
+    hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/hailctl-test/{{ token }}
+
+    mkdir -p foo
+    echo "bar" > foo/baz.txt
+
+    cat >simple_hail.py <<EOF
+    import hail as hl
+
+    with open('foo/baz.txt') as f:
+        print(f.read())
+
+    hl.init(app_name='test-hailctl-batch-submit-query')
+    hl.utils.range_table(10).collect()
+    EOF
+
+    # https://stackoverflow.com/questions/3524978/logging-functions-in-bash-and-stdout 
+    exec 3>&1
+
+    function log { echo "$@" 1>&3; }
+
+    function submit {
+      local status=$(hailctl batch submit --quiet --output json --wait "$@")
+      log "$status"
+      log $(hailctl batch log -o json $(jq -jr '.batch_id' <<< "$status") 1)  # print the job log
+      test $(jq -jr '.state' <<< "$status") = "Success"
+    }
+
+    submit -v simple_hail.py:/ -v foo/:/foo/ --workdir / --name=test-hailctl-batch-submit python3 simple_hail.py
+
+    cat >hail_with_args.py <<EOF
+    import hail as hl
+    import sys
+
+    with open('foo/baz.txt') as f:
+        print(f.read())
+
+    hl.init(app_name='test-hailctl-batch-submit-query')
+    assert hl.utils.range_table(int(sys.argv[1]))._force_count() == 100
+    EOF
+
+    submit -v hail_with_args.py:/ -v foo/:/foo/ --workdir / --name=test-hailctl-batch-submit python3 hail_with_args.py 100
+
+    cat >file.sh <<EOF
+    set -ex
+
+    cat foo/baz.txt
+    echo "Hello World!"
+    EOF
+
+    submit --shell /bin/sh --name=test-hailctl-batch-submit -v file.sh:/ -v foo/:/foo/ -o json --image busybox:latest sh file.sh
+
+    cat >file-with-args.sh <<EOF
+    [ "$#" -eq 2 ]
+
+    cat foo/baz.txt
+    echo "Hello World! $1 $2"
+    EOF
+
+    submit --name=test-hailctl-batch-submit -v file-with-args.sh:/ -v foo/:/foo/ -o json --image ubuntu:latest sh file-with-args.sh abc 123
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - hailgenetics_hail_image
+  - upload_query_jar
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - merge_code
+  - deploy_batch
+- kind: runImage
+  name: test_batch_docs
+  image:
+    valueFrom: hail_dev_image.image
+  script: |
+    set -ex
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    hailctl config set batch/billing_project test
+    hailctl config set batch/remote_tmpdir {{ global.test_storage_uri }}/test_batch_docs/{{ token }}/
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --doctest-modules \
+            --doctest-glob='*.rst' \
+            --doctest-continue-on-failure \
+            --ignore=docs/cookbook/files/ \
+            --timeout=120 \
+            --ignore=docs/conf.py \
+            /io/hailtop/batch
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - hail_dev_image
+  - merge_code
+  - deploy_batch
+  timeout: 1200
+  inputs:
+  - from: /repo/hail/python/hailtop
+    to: /io/hailtop
+- kind: runImage
+  name: cleanup_ci_test_repo
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: hail_ubuntu_image.image
+  script: |
+    set -e
+    TOKEN=$(cat /secret/ci-secrets/user1)
+    echo deleting ci-test-{{ create_ci_test_repo.token }}...
+    curl -XDELETE \
+      -ifsSL \
+      https://api.github.com/repos/hail-ci-test/ci-test-{{ create_ci_test_repo.token }} \
+      -H "Authorization: token ${TOKEN}"
+  secrets:
+  - name: hail-ci-0-1-service-account-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /secret/ci-secrets
+  alwaysRun: true
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - default_ns
+  - hail_ubuntu_image
+  - create_ci_test_repo
+  - deploy_ci
+  - test_ci
+- kind: runImage
+  name: test_dataproc-37
+  image:
+    valueFrom: ci_utils_image.image
+  resources:
+    preemptible: False
+  script: |
+    set -ex
+
+    cd /io/repo
+
+    gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
+    gcloud config set project hail-vdc
+    gcloud config set dataproc/region us-central1
+
+    if git ls-remote --exit-code --tags origin $(cat hail/env/HAIL_PIP_VERSION)
+    then
+        echo "tag $HAIL_PIP_VERSION already exists"
+        exit 0
+    fi
+
+    cd hail
+    make test-dataproc-37 HAIL_BUILD_MODE=Release \
+        -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
+  dependsOn:
+  - ci_utils_image
+  - default_ns
+  - merge_code
+  - upload_temporary_hailctl_artifacts
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/hail/build/deploy/dist
+  secrets:
+  - name: test-dataproc-service-account-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dataproc-service-account-key
+  scopes:
+  - deploy
+  - dev
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_dataproc-38
+  image:
+    valueFrom: ci_utils_image.image
+  resources:
+    preemptible: False
+  script: |
+    set -ex
+
+    cd /io/repo
+
+    gcloud auth activate-service-account --key-file=/test-dataproc-service-account-key/test-dataproc-service-account-key.json
+    gcloud config set project hail-vdc
+    gcloud config set dataproc/region us-central1
+
+    if git ls-remote --exit-code --tags origin $(cat hail/env/HAIL_PIP_VERSION)
+    then
+        echo "tag $HAIL_PIP_VERSION already exists"
+        exit 0
+    fi
+
+    cd hail
+    make test-dataproc-38 HAIL_BUILD_MODE=Release \
+        -o $(ls build/deploy/dist/hail-*-py3-none-any.whl)
+  dependsOn:
+  - ci_utils_image
+  - default_ns
+  - merge_code
+  - upload_temporary_hailctl_artifacts
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/repo/hail/build/deploy/dist
+  scopes:
+  - deploy
+  - dev
+  clouds:
+  - gcp
+- kind: runImage
+  name: release
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    cd /io
+
+    gcloud auth activate-service-account --key-file=/ci-deploy-0-1--hail-is-hail/ci-deploy-0-1--hail-is-hail.json
+
+    gcloud auth -q configure-docker {{ global.docker_prefix.split('/')[0] }}
+    cat /docker-hub-hailgenetics/password | skopeo login --username hailgenetics --password-stdin docker.io
+
+    cp /pypi-credentials/pypirc $HOME/.pypirc
+    printf 'Authorization: token ' > github-oauth
+    cat /hail-ci-0-1-github-oauth-token/oauth-token >>github-oauth
+    printf '#!/bin/bash\necho ' > git-askpass
+    cat /hail-ci-0-1-github-oauth-token/oauth-token >>git-askpass
+    chmod 755 git-askpass
+    export GIT_ASKPASS=/io/git-askpass
+
+    cd /io/repo/hail
+    export HAIL_PIP_VERSION=$(cat env/HAIL_PIP_VERSION)
+
+    if git ls-remote --exit-code --tags origin $HAIL_PIP_VERSION
+    then
+        echo "tag $HAIL_PIP_VERSION already exists"
+        echo '0' > /io/release-hail-flag
+        exit 0
+    fi
+
+    # #14452 - must build wheel with release `hailtop/hailctl/deploy.yaml`
+    # use `-o` to prevent `mill` from rebuilding the "SHADOW_JAR"
+    make upload-artifacts HAIL_BUILD_MODE=Release DEPLOY_REMOTE=origin \
+      -o out/hail/2.12/assembly.dest/out.jar
+
+    echo Setting arguments and invoking release.sh.
+
+    HAIL_VERSION=$(cat env/HAIL_VERSION) \
+    WHEEL="build/deploy/dist/hail-${HAIL_PIP_VERSION}-py3-none-any.whl" \
+    GIT_VERSION=$(cat env/REVISION) \
+    REMOTE=origin \
+    GITHUB_OAUTH_HEADER_FILE=/io/github-oauth \
+    HAIL_GENETICS_HAIL_IMAGE=docker://{{ hailgenetics_hail_image.image }} \
+    HAIL_GENETICS_HAIL_IMAGE_PY_3_10=docker://{{ hailgenetics_hail_image_python_3_10.image }} \
+    HAIL_GENETICS_HAIL_IMAGE_PY_3_11=docker://{{ hailgenetics_hail_image.image }} \
+    HAIL_GENETICS_HAIL_IMAGE_PY_3_12=docker://{{ hailgenetics_hail_image_python_3_12.image }} \
+    HAIL_GENETICS_HAIL_IMAGE_PY_3_13=docker://{{ hailgenetics_hail_image_python_3_13.image }} \
+    HAIL_GENETICS_HAILTOP_IMAGE=docker://{{ hailgenetics_hailtop_image.image }} \
+    HAIL_GENETICS_VEP_GRCH37_85_IMAGE=docker://{{ hailgenetics_vep_grch37_85_image.image }} \
+    HAIL_GENETICS_VEP_GRCH38_95_IMAGE=docker://{{ hailgenetics_vep_grch38_95_image.image }} \
+    WEBSITE_TAR=/io/www.tar.gz \
+    bash scripts/release.sh
+
+    echo '1' > /io/release-hail-flag
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/release/hail/out/hail/2.12/assembly.dest/out.jar
+    to: /io/repo/hail/out/hail/2.12/assembly.dest/out.jar
+  - from: /www.tar.gz
+    to: /io/www.tar.gz
+  outputs:
+  - from: /io/release-hail-flag
+    to: /release-hail-flag
+  secrets:
+  - name: pypi-credentials
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /pypi-credentials
+  - name: ci-deploy-0-1--hail-is-hail
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /ci-deploy-0-1--hail-is-hail
+  - name: docker-hub-hailgenetics
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /docker-hub-hailgenetics
+  - name: hail-ci-0-1-github-oauth-token
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /hail-ci-0-1-github-oauth-token
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - merge_code
+  - hailgenetics_hail_image
+  - hailgenetics_hail_image_python_3_10
+  - hailgenetics_hail_image_python_3_12
+  - hailgenetics_hail_image_python_3_13
+  - hailgenetics_hailtop_image
+  - hailgenetics_vep_grch37_85_image
+  - hailgenetics_vep_grch38_95_image
+  - build_hail_jar_and_wheel
+  - test_hail_java
+  - test_hail_python
+  - test_hailtop_python
+  - test_hail_python_local_backend
+  - test_hail_python_service_backend_gcp
+  - test_hail_scala_fs
+  - test_hail_services_java
+  - test_hail_spark_conf_requester_pays_parsing
+  - test_dataproc-37
+  - test_dataproc-38
+  - make_docs
+  clouds:
+  - gcp
+- kind: runImage
+  name: deploy_wheel
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    gcloud auth activate-service-account --key-file=/gsa-key/key.json
+    HAIL_WHEEL_FILE=hail-$(cat /io/repo/hail/env/HAIL_PIP_VERSION)-py3-none-any.whl
+    gcloud storage cp "/io/wheel/$HAIL_WHEEL_FILE" "gs://cpg-hail-ci/wheels/$HAIL_WHEEL_FILE"
+  inputs:
+  - from: /repo
+    to: /io/repo
+  - from: /derived/release/hail/build/deploy/dist
+    to: /io/wheel
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - build_hail_jar_and_wheel
+  clouds:
+  - gcp
+- kind: runImage
+  name: deploy_hailgenetics_image
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    gcloud auth -q configure-docker australia-southeast1-docker.pkg.dev
+    skopeo copy docker://{{ hailgenetics_hail_image.image }} docker://australia-southeast1-docker.pkg.dev/hail-295901/hail/hailgenetics/hail:$(cat /io/repo/hail/env/HAIL_PIP_VERSION)
+    skopeo copy docker://{{ hailgenetics_hailtop_image.image }} docker://australia-southeast1-docker.pkg.dev/hail-295901/hail/hailgenetics/hailtop:$(cat /io/repo/hail/env/HAIL_PIP_VERSION)
+  inputs:
+  - from: /repo
+    to: /io/repo
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - hailgenetics_hail_image
+  - hailgenetics_hailtop_image
+  clouds:
+  - gcp
+- kind: runImage
+  name: make_terra_prs
+  image:
+    valueFrom: ci_utils_image.image
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - release
+  inputs:
+  - from: /release-hail-flag
+    to: /io/release-hail-flag
+  - from: /repo
+    to: /io/repo
+  secrets:
+  - name: hail-ci-0-1-github-oauth-token
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /hail-ci-0-1-github-oauth-token
+  clouds:
+  - gcp
+  scopes:
+  - deploy
+  - dev
+  script: |
+    set -ex
+    if [[ $(< /io/release-hail-flag) != '1' ]]
+    then
+        echo 'Skipping making terra update prs (no new release published)'
+        exit 0
+    fi
+
+    printf 'Authorization: token ' > github-oauth
+    cat /hail-ci-0-1-github-oauth-token/oauth-token >> /io/github-oauth
+    printf '#!/bin/bash\necho ' > git-askpass
+    cat /hail-ci-0-1-github-oauth-token/oauth-token >> /io/git-askpass
+    chmod 755 /io/git-askpass
+    export GIT_ASKPASS=/io/git-askpass
+
+    cd /io/repo/hail
+    export HAIL_PIP_VERSION=$(cat env/HAIL_PIP_VERSION)
+    export GITHUB_OAUTH_HEADER_FILE=/io/github-oauth
+    bash scripts/make-terra-prs.sh
+- kind: runImage
+  name: mirror_hailgenetics_images
+  image: quay.io/skopeo/stable:v1.13.2
+  script: |
+    set -ex
+
+    REGISTRY={{ global.docker_prefix.split('/')[0] }}
+
+    set +x
+    {% if global.cloud == "gcp" %}
+    cat $GOOGLE_APPLICATION_CREDENTIALS | base64 -w 0 | skopeo login -u _json_key_base64 --password-stdin $REGISTRY
+    {% else %}
+    echo "unknown cloud {{ global.cloud }}"
+    exit 1
+    {% endif %}
+    set -x
+
+    cd /io/docker/hailgenetics
+    export HAIL_PIP_VERSION=$(cat /io/HAIL_PIP_VERSION)
+    export DOCKER_PREFIX={{ global.docker_prefix }}
+    {% if global.dockerhub_prefix %}
+    export DOCKERHUB_PREFIX={{ global.dockerhub_prefix }}
+    {% endif %}
+    bash mirror_images.sh
+  inputs:
+  - from: /repo/hail/env/HAIL_PIP_VERSION
+    to: /io/HAIL_PIP_VERSION
+  - from: /repo/docker/hailgenetics/mirror_images.sh
+    to: /io/docker/hailgenetics/mirror_images.sh
+  - from: /repo/docker/copy_image.sh
+    to: /io/docker/copy_image.sh
+  scopes:
+  - deploy
+  - dev
+  dependsOn:
+  - default_ns
+  - merge_code
+- kind: buildImage2
+  name: website_image
+  dockerFile: /io/repo/website/Dockerfile
+  contextPath: /io/repo
+  publishAs: website
+  inputs:
+  - from: /repo/website
+    to: /io/repo/website
+  - from: /docs.tar.gz
+    to: /io/repo/docs.tar.gz
+  - from: /repo/hail/python/setup-hailtop.py
+    to: /io/repo/hail/python/setup-hailtop.py
+  - from: /repo/hail/python/MANIFEST.in
+    to: /io/repo/hail/python/MANIFEST.in
+  - from: /repo/hail/python/hailtop
+    to: /io/repo/hail/python/hailtop
+  - from: /repo/gear
+    to: /io/repo/gear
+  - from: /repo/web_common
+    to: /io/repo/web_common
+  dependsOn:
+  - hail_ubuntu_image
+  - get_pip_versioned_docs
+  clouds:
+  - gcp
+  resources:
+    storage: 20Gi
+    cpu: "2"
+    memory: standard
+- kind: deploy
+  name: deploy_website
+  namespace:
+    valueFrom: default_ns.name
+  config: website/deployment.yaml
+  wait:
+  - kind: Service
+    name: www
+    for: alive
+  dependsOn:
+  - default_ns
+  - website_image
+  - create_certs
+  - create_session_key
+  - create_deploy_config
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_website
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    set -ex
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    hailctl curl {{ default_ns.name }} www / \
+            -vvv \
+            -fsSL \
+            --retry 3 \
+            --retry-delay 5
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  dependsOn:
+  - default_ns
+  - create_accounts
+  - hailgenetics_hailtop_image
+  - deploy_website
+  clouds:
+  - gcp
+- kind: runImage
+  name: test_hail_scala_fs
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+    cd /io
+    mkdir -p src/test
+    tar xzf resources.tar.gz -C src/test
+
+    export HAIL_CLOUD={{ global.cloud }}
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-gsa-key/key.json
+    export HAIL_FS_TEST_CLOUD_RESOURCES_URI={{ global.test_storage_uri }}/{{ upload_test_resources_to_blob_storage.token }}/test/resources/fs
+    export HAIL_TEST_STORAGE_URI={{ global.test_storage_uri }}
+
+    set +e
+    java -Xms7500M -Xmx7500M \
+         -cp hail-test.jar:$SPARK_HOME/jars/* \
+         org.testng.TestNG \
+         -listener is.hail.LogTestListener \
+         testng-fs.xml
+    exit_code=$?
+    set -e
+    if [[ $exit_code -eq 2 ]]
+    then
+        echo "some tests were skipped, but exiting success anyway"
+        exit 0
+    else
+        exit $exit_code
+    fi
+  inputs:
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
+    to: /io/hail-test.jar
+  - from: /repo/hail/testng-fs.xml
+    to: /io/testng-fs.xml
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  timeout: 1200
+  dependsOn:
+  - default_ns
+  - create_certs
+  - create_accounts
+  - hail_run_image
+  - build_debug_hail_test_jar
+  - build_hail_test_artifacts
+  - upload_test_resources_to_blob_storage
+- kind: runImage
+  name: test_hail_services_java
+  image:
+    valueFrom: hail_run_image.image
+  resources:
+    memory: standard
+    cpu: '2'
+  script: |
+    set -ex
+
+    export HAIL_CLOUD={{ global.cloud }}
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+
+    cd /io
+    mkdir -p src/test
+    tar xzf resources.tar.gz -C src/test
+    java -Xms7500M -Xmx7500M \
+         -cp hail-test.jar:$SPARK_HOME/jars/* \
+         org.testng.TestNG \
+         -listener is.hail.LogTestListener \
+         testng-services.xml
+  inputs:
+  - from: /resources.tar.gz
+    to: /io/resources.tar.gz
+  - from: /derived/debug/hail/out/hail/2.12/test/assembly.dest/out.jar
+    to: /io/hail-test.jar
+  - from: /repo/hail/testng-services.xml
+    to: /io/testng-services.xml
+  secrets:
+  - name: test-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-gsa-key
+  timeout: 1200
+  dependsOn:
+  - default_ns
+  - create_certs
+  - create_accounts
+  - hail_run_image
+  - build_debug_hail_test_jar
+  - build_hail_test_artifacts
+  - upload_query_jar
+  - deploy_batch
+- kind: runImage
+  name: start_hail_benchmark
+  scopes:
+  - deploy
+  - dev
+  clouds:
+  - gcp
+  dependsOn:
+  - default_ns
+  - hail_dev_image
+  - release
+  image:
+    valueFrom: hail_dev_image.image
+  inputs:
+  - from: /repo/hail/python
+    to: /io/repo/hail/python
+  - from: /repo/hail/env
+    to: /io/repo/hail/env
+  - from: /repo/hail/scripts/benchmark_in_batch.py
+    to: /io/repo/hail/scripts/benchmark_in_batch.py
+  - from: /release-hail-flag
+    to: /io/release-hail-flag
+  script: |
+    set -ex
+
+    # only run benchmarks iff we've published a new release
+    if [[ $(< /io/release-hail-flag) != '1' ]]
+    then
+        echo 'Skipping benchmarks (no new release published).'
+        exit 0
+    fi
+
+    pushd /io/repo/hail
+
+    BUCKET=hail-benchmarks-2
+    HAIL_VERSION=$(cat env/HAIL_VERSION)
+    RESULTS_PREFIX="gs://${BUCKET}/{{ scope }}/${HAIL_VERSION}"
+
+    export HAIL_BATCH_REGIONS={{ global.gcp_region }}
+    export HAIL_BATCH_BILLING_PROJECT=benchmark
+    export HAIL_BATCH_REMOTE_TMPDIR={{ ci_storage_uri }}/{{ token }}
+
+    PYTHONPATH="$PWD/python" python3 ./scripts/benchmark_in_batch.py submit \
+        {{ hail_dev_image.image }} \
+        $RESULTS_PREFIX \
+        $HAIL_VERSION
+
+- kind: runImage
+  name: cancel_all_running_test_batches
+  image:
+    valueFrom: hailgenetics_hailtop_image.image
+  script: |
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+
+    cat >cancel_all_running_test_batches.py <<'EOF'
+    from hailtop.batch_client.aioclient import BatchClient
+    import asyncio
+    import traceback
+
+    async def cancel_all(query):
+        bc = await BatchClient.create('test')
+        async for b in bc.list_batches(query):
+            status = await b.last_known_status()
+            print(status)
+            try:
+                await b.cancel()
+            except:
+                traceback.print_exc()
+
+    asyncio.get_event_loop().run_until_complete(cancel_all('user:test running'))
+    EOF
+
+    python3 cancel_all_running_test_batches.py
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  alwaysRun: true
+  timeout: 300
+  dependsOn:
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - hailgenetics_hailtop_image
+  - deploy_batch
+  - test_batch
+  - test_ci
+  - test_hailtop_python
+  - test_hail_python_service_backend_gcp
+  - test_hail_services_java
+  - test_batch_docs
+  - test_hailctl_batch
+- kind: runImage
+  name: test_batch_invariants
+  image:
+    valueFrom: hail_dev_image.image
+  script: |
+    export GOOGLE_APPLICATION_CREDENTIALS=/test-dev-gsa-key/key.json
+    export HAIL_DEFAULT_NAMESPACE={{ default_ns.name }}
+    export DOCKER_PREFIX="{{ global.docker_prefix }}"
+    export DOCKER_ROOT_IMAGE="{{ global.docker_root_image }}"
+    python3 -m pytest \
+            -Werror:::hail -Werror:::hailtop -Werror::ResourceWarning \
+            --log-cli-level=INFO \
+            -s \
+            -r A \
+            -vv \
+            --instafail \
+            --durations=50 \
+            --log-date-format="%Y-%m-%dT%H:%M:%S" \
+            --log-format="%(asctime)s %(levelname)s %(name)s %(filename)s:%(lineno)d:%(funcName)s %(message)s" \
+            --timeout=120 \
+            /io/test/test_invariants.py
+  inputs:
+  - from: /repo/batch/test
+    to: /io/test
+  timeout: 300
+  secrets:
+  - name: test-dev-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /test-dev-gsa-key
+  scopes:
+  - test
+  - dev
+  dependsOn:
+  - create_deploy_config
+  - create_accounts
+  - default_ns
+  - merge_code
+  - hail_dev_image
+  - deploy_batch
+  - test_batch
+  - test_ci
+  - test_hailtop_python
+  - test_hail_python_service_backend_gcp
+  - cancel_all_running_test_batches
+- kind: runImage
+  name: delete_gcp_batch_instances
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  alwaysRun: true
+  script: |
+    set -ex
+    gcloud -q auth activate-service-account --key-file=/batch-gsa-key/key.json
+    set +e
+    kubectl -n {{ default_ns.name }} scale deployment batch-driver --replicas=0
+    gcloud -q compute instances list \
+        --filter 'tags.items=batch2-agent AND labels.namespace={{ default_ns.name }}' \
+        --format="table[no-heading](zone.basename(), name)" \
+        --project {{ global.gcp_project }} \
+      | xargs -P8 -n2 -r sh -c 'gcloud -q compute instances delete --zone "$1" --project {{ global.gcp_project }} "$2" || true' argv0
+    gcloud -q compute disks list \
+        --filter 'labels.batch=1 AND labels.namespace={{ default_ns.name }}' \
+        --format="table[no-heading](zone.basename(), name)" \
+        --project {{ global.gcp_project }} \
+      | xargs -P8 -n2 -r sh -c 'gcloud -q compute disks delete --zone "$1" --project {{ global.gcp_project }} "$2" || true' argv0
+  secrets:
+  - name: batch-gsa-key
+    namespace:
+      valueFrom: default_ns.name
+    mountPath: /batch-gsa-key
+  scopes:
+  - dev
+  - test
+  serviceAccount:
+    name: admin
+    namespace:
+      valueFrom: default_ns.name
+  clouds:
+  - gcp
+  dependsOn:
+  - default_ns
+  - ci_utils_image
+  - test_batch_invariants
+  - test_batch
+  - test_ci
+  - test_hailtop_python
+  - test_hail_python_service_backend_gcp
+  - cancel_all_running_test_batches
+- kind: runImage
+  name: setup_dev_namespace_autoscaledown
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    {% for user in code.get("developers", []) %}
+    {% if user['username'] != 'test-dev' %}
+
+    if kubectl get namespace {{ user["username"] }} 2>/dev/null
+    then
+    cat > the.yaml <<'EOF'
+    apiVersion: batch/v1
+    kind: CronJob
+    metadata:
+      name: dev-namespace-scaledown-{{ user["username"] }}
+      namespace: {{ user["username"] }}
+    spec:
+      schedule: "0 0 * * *"  # Every day at midnight UTC
+      concurrencyPolicy: Forbid
+      successfulJobsHistoryLimit: 1
+      failedJobsHistoryLimit: 1
+      jobTemplate:
+        spec:
+          template:
+            spec:
+              serviceAccountName: admin
+              containers:
+              - name: dev-namespace-scaledown-{{ user["username"] }}
+                image: bitnami/kubectl:latest
+                command:
+                - /bin/sh
+                - -c
+                - set -ex ; kubectl scale deployments --all -n {{ user["username"] }} --replicas=0 && kubectl scale statefulsets --all -n {{ user["username"] }} --replicas=0
+              restartPolicy: OnFailure
+    EOF
+
+    kubectl apply -f the.yaml
+    echo "For {{ user["username"] }}, applied:"
+    echo "---"
+    cat the.yaml
+    else
+    echo "Skipping {{ user["username"] }} because they have no namespace."
+    fi
+
+    {% endif %}
+    {% endfor %}
+  scopes:
+  - deploy
+  serviceAccount:
+    name: ci-agent
+    namespace:
+      valueFrom: default_ns.name
+  dependsOn:
+  - ci_utils_image
+  - default_ns
+- kind: runImage
+  name: test_gcp_ar_cleanup_policies
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  script: |
+    set -ex
+    cd /io/repo/
+    new_policy=$(mktemp)
+    python3 devbin/generate_gcp_ar_cleanup_policy.py > $new_policy
+    diff $new_policy infra/gcp-broad/gcp-ar-cleanup-policy.txt || {
+      echo '>>> AR cleanup policy has changed, new policy is <<<'
+      cat $new_policy
+      echo '--------------------------------------'
+      echo "Please regenerate the policy file by running:"
+      echo "> python3 devbin/generate_gcp_ar_cleanup_policy.py > infra/gcp-broad/gcp-ar-cleanup-policy.txt"
+      exit 1
+    }
+  inputs:
+  - from: /repo/build.yaml
+    to: /io/repo/build.yaml
+  - from: /repo/devbin
+    to: /io/repo/devbin
+  - from: /repo/infra
+    to: /io/repo/infra
+  - from: /repo/docker
+    to: /io/repo/docker
+  - from: /repo/ci/test/resources
+    to: /io/repo/ci/test/resources
+  clouds:
+  - gcp
+  dependsOn:
+  - ci_utils_image
+  - default_ns
+- kind: runImage
+  name: set_gcp_ar_cleanup_policies
+  resources:
+    memory: standard
+    cpu: '0.25'
+  image:
+    valueFrom: ci_utils_image.image
+  scopes:
+  - deploy
+  script: |
+    gcloud artifacts repositories set-cleanup-policies hail \
+      --project={{ global.gcp_project }} \
+      --location=us \
+      --policy=/io/repo/infra/gcp-broad/gcp-ar-cleanup-policy.txt \
+      --no-dry-run
+  inputs:
+  - from: /repo/infra
+    to: /io/repo/infra
+  clouds:
+  - gcp
+  dependsOn:
+  - test_gcp_ar_cleanup_policies
+  - ci_utils_image
diff --git a/ci/Dockerfile.ci-utils b/ci/Dockerfile.ci-utils
index 68a6bdb83f2..33b6fdc0980 100644
--- a/ci/Dockerfile.ci-utils
+++ b/ci/Dockerfile.ci-utils
@@ -11,7 +11,7 @@ RUN hail-pip-install \
       'twine>=6.2.0,<7' \
       'Jinja2>3,<4'
 
-FROM golang:1.18 AS skopeo-build
+FROM {% if global.dockerhub_prefix %}{{ global.dockerhub_prefix }}/library/{% endif %}golang:1.18 AS skopeo-build
 
 WORKDIR /usr/src/skopeo
 
diff --git a/ci/ci/envoy.py b/ci/ci/envoy.py
index 0cf85fe9c17..9902171f832 100644
--- a/ci/ci/envoy.py
+++ b/ci/ci/envoy.py
@@ -83,29 +83,6 @@ def gateway_default_host(service: Service, domain: str) -> dict:
     if service.name == 'www':
         domains.append(domain)
 
-    if service.name == 'ukbb-rg':
-        return {
-            '@type': 'type.googleapis.com/envoy.config.route.v3.VirtualHost',
-            'name': service.name,
-            'domains': domains,
-            'routes': [
-                {
-                    'match': {'prefix': '/rg_browser'},
-                    'route': route_to_cluster('ukbb-rg-browser'),
-                    'typed_per_filter_config': {
-                        'envoy.filters.http.ext_authz': auth_check_exemption(),
-                    },
-                },
-                {
-                    'match': {'prefix': '/'},
-                    'route': route_to_cluster('ukbb-rg-static'),
-                    'typed_per_filter_config': {
-                        'envoy.filters.http.ext_authz': auth_check_exemption(),
-                    },
-                },
-            ],
-        }
-
     return {
         '@type': 'type.googleapis.com/envoy.config.route.v3.VirtualHost',
         'name': service.name,
@@ -237,15 +214,7 @@ def clusters(
 ) -> List[dict]:
     clusters = []
     for service in default_services:
-        if service.name == 'ukbb-rg':
-            browser_cluster = make_cluster('ukbb-rg-browser', 'ukbb-rg-browser.ukbb-rg', proxy, verify_ca=True)
-            static_cluster = make_cluster('ukbb-rg-static', 'ukbb-rg-static.ukbb-rg', proxy, verify_ca=True)
-            clusters.append(browser_cluster)
-            clusters.append(static_cluster)
-        else:
-            clusters.append(
-                make_cluster(service.name, f'{service.name}.default.svc.cluster.local', proxy, verify_ca=True)
-            )
+        clusters.append(make_cluster(service.name, f'{service.name}.default.svc.cluster.local', proxy, verify_ca=True))
 
     for namespace, services in internal_services_per_namespace.items():
         for service in services:
diff --git a/ci/ci/templates/batch.html b/ci/ci/templates/batch.html
index 1b2d6ae75ab..d20df0dfb2e 100644
--- a/ci/ci/templates/batch.html
+++ b/ci/ci/templates/batch.html
@@ -2,7 +2,7 @@
 {% extends "layout.html" %}
 {% block title %}Batch {{ batch['id'] }}{% endblock %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+    <script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 {% block content %}
     <h1>Batch {{ batch['id'] }}</h1>
diff --git a/ci/ci/templates/dev-deploy-table.html b/ci/ci/templates/dev-deploy-table.html
index edfd9663118..0ff92ae0015 100644
--- a/ci/ci/templates/dev-deploy-table.html
+++ b/ci/ci/templates/dev-deploy-table.html
@@ -1,10 +1,10 @@
 {% macro dev_deploy_table(dev_deploys) %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/search_bar.js"></script>
-    <script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+    <script defer src="{{ base_path }}/common_static/search_bar.js"></script>
+    <script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 <div class="searchbar-table">
-  <input type="text" id="devDepSearchBar" onkeyup="searchTable('dev-deploys', 'devDepSearchBar')" placeholder="Search terms...">
+  <input type="text" id="devDepSearchBar" name="searchbar-input" data-table-id="dev-deploys" placeholder="Search terms...">
   <table id="dev-deploys" class="data-table">
     <thead>
       <th>ID</th>
diff --git a/ci/ci/templates/index.html b/ci/ci/templates/index.html
index 1694005c760..1a47d232155 100644
--- a/ci/ci/templates/index.html
+++ b/ci/ci/templates/index.html
@@ -2,8 +2,8 @@
 {% extends "layout.html" %}
 {% block title %}CI{% endblock %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/search_bar.js"></script>
-    <script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+    <script defer src="{{ base_path }}/common_static/search_bar.js"></script>
+    <script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 {% block content %}
     <h1>CI</h1>
@@ -71,7 +71,4 @@ <h2>Authorize SHA</h2>
       <input type="text" name="sha" id="sha">
       <button type="submit">Authorize</button>
     </form>
-    <script type="text/javascript">
-      focusOnSlash("prsSearchBar");
-    </script>
 {% endblock %}
diff --git a/ci/ci/templates/job-table.html b/ci/ci/templates/job-table.html
index ca7b2dcf2d9..e9fefb27c92 100644
--- a/ci/ci/templates/job-table.html
+++ b/ci/ci/templates/job-table.html
@@ -1,9 +1,9 @@
 {% macro job_table(jobs, id, searchBarId) %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/search_bar.js"></script>
+    <script defer src="{{ base_path }}/common_static/search_bar.js"></script>
 {% endblock %}
 <div class="searchbar-table">
-  <input type="text" id="{{ searchBarId }}" onkeyup="searchTable('{{ id }}', '{{ searchBarId }}')" placeholder="Search terms...">
+  <input type="text" id="{{ searchBarId }}" name="searchbar-input" data-table-id="{{ id }}" placeholder="Search terms...">
   <table id="{{ id }}" class="data-table" style="line-height: 175%">
     <thead>
       <tr>
diff --git a/ci/ci/templates/pr-table.html b/ci/ci/templates/pr-table.html
index 587653b1b7f..fef706e67da 100644
--- a/ci/ci/templates/pr-table.html
+++ b/ci/ci/templates/pr-table.html
@@ -1,6 +1,6 @@
 {% macro pr_table(wb, id, searchBarId) %}
 <div class="searchbar-table">
-  <input type="text" id="{{ searchBarId }}" onkeyup="searchTable('{{ id }}', '{{ searchBarId }}')" placeholder="Search terms..."/>
+  <input type="text" id="{{ searchBarId }}" name="searchbar-input" data-table-id="{{ id }}" placeholder="Search terms..."/>
   <table id="{{ id }}" class="data-table">
   <thead>
     <tr>
diff --git a/ci/ci/templates/pr.html b/ci/ci/templates/pr.html
index 58719e6d8a1..1e8c2fc9d13 100644
--- a/ci/ci/templates/pr.html
+++ b/ci/ci/templates/pr.html
@@ -2,7 +2,7 @@
 {% extends "layout.html" %}
 {% block title %}PR {{ number }}{% endblock %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+    <script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 {% block content %}
     <h1>{{ pr.title }} <a rel="noopener" href="https://github.com/{{ repo }}/pull/{{ pr.number }}"><span class="gh-number">#{{ pr.number }}</span></a></h1>
diff --git a/ci/pinned-requirements.txt b/ci/pinned-requirements.txt
index a3d51674383..476bdd11279 100644
--- a/ci/pinned-requirements.txt
+++ b/ci/pinned-requirements.txt
@@ -1,6 +1,6 @@
 # This file was autogenerated by uv via the following command:
 #    uv pip compile --python-version 3.10 --python-platform linux ci/requirements.txt --output-file=ci/pinned-requirements.txt
-certifi==2025.11.12
+certifi==2026.1.4
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
@@ -8,6 +8,7 @@ certifi==2025.11.12
     #   requests
 cffi==2.0.0
     # via
+    #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   cryptography
@@ -22,8 +23,9 @@ click==8.3.1
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   zulip
-cryptography==46.0.3
+cryptography==46.0.5
     # via
+    #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   pyjwt
 distro==1.9.0
@@ -37,12 +39,13 @@ idna==3.11
     #   -c ci/../hail/python/pinned-requirements.txt
     #   -c ci/../web_common/pinned-requirements.txt
     #   requests
-pycparser==2.23
+pycparser==3.0
     # via
+    #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
     #   -c ci/../hail/python/pinned-requirements.txt
     #   cffi
-pyjwt==2.10.1
+pyjwt==2.11.0
     # via
     #   -c ci/../hail/python/pinned-requirements.txt
     #   gidgethub
@@ -64,7 +67,7 @@ uritemplate==4.2.0
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   gidgethub
-urllib3==2.5.0
+urllib3==2.6.3
     # via
     #   -c ci/../gear/pinned-requirements.txt
     #   -c ci/../hail/python/dev/pinned-requirements.txt
diff --git a/config.mk b/config.mk
index 445f6ac42c9..707af4b4d52 100644
--- a/config.mk
+++ b/config.mk
@@ -4,10 +4,13 @@
 
 ifdef NAMESPACE
 DOCKER_PREFIX = $(eval DOCKER_PREFIX := $$(shell kubectl -n $(NAMESPACE) get secret global-config --template={{.data.docker_prefix}} | base64 --decode))$(DOCKER_PREFIX)
+DOCKERHUB_PREFIX = $(eval DOCKERHUB_PREFIX := $$(shell kubectl -n $(NAMESPACE) get secret global-config --template={{.data.dockerhub_prefix}} 2>/dev/null | base64 --decode || echo))$(DOCKERHUB_PREFIX)
 else
 DOCKER_PREFIX = docker.io
+DOCKERHUB_PREFIX =
 endif
 
+
 DOMAIN = $(eval DOMAIN := $$(shell kubectl -n $(NAMESPACE) get secret global-config --template={{.data.domain}} | base64 --decode))$(DOMAIN)
 CLOUD = $(eval CLOUD := $$(shell kubectl -n $(NAMESPACE) get secret global-config --template={{.data.cloud}} | base64 --decode))$(CLOUD)
 AZURE_SUBSCRIPTION_ID = $(eval AZURE_SUBSCRIPTION_ID := $$(shell kubectl -n $(NAMESPACE) get secret global-config --template={{.data.azure_subscription_id}} | base64 --decode))$(AZURE_SUBSCRIPTION_ID)
diff --git a/dev-docs/hail-overview.md b/dev-docs/hail-overview.md
index 5a3156dc061..12e6010e90b 100644
--- a/dev-docs/hail-overview.md
+++ b/dev-docs/hail-overview.md
@@ -118,7 +118,6 @@ Other:
 * $HAIL/datasets: ETL code for the Hail Query Datasets API
 * $HAIL/docker: base docker images used by services
 * $HAIL/hail/python/hailtop/hailctl: implementation of the hailctl command-line tool
-* $HAIL/ukbb-rg: UKBB genetic correlation browser configuration, available at https://ukbb-rg.hail.is/
 
 ## Hail Query Java/Scala Code Organization
 
diff --git a/dev-docs/refreshing-trivy-scanner-github-secret.md b/dev-docs/refreshing-trivy-scanner-github-secret.md
new file mode 100644
index 00000000000..e5222b498ca
--- /dev/null
+++ b/dev-docs/refreshing-trivy-scanner-github-secret.md
@@ -0,0 +1,90 @@
+# Refreshing the trivy-scanner GitHub Secret
+
+The `GOOGLE_GAR_CREDENTIALS` GitHub secret is used by the Trivy Security Scan workflow
+(`.github/workflows/trivy-scan.yml`) to authenticate with Google Cloud and access
+images from Google Artifact Registry (GAR) for vulnerability scanning.
+
+This secret contains a Google Service Account (GSA) key in JSON format. Service account
+keys should be rotated periodically for security. This guide walks through the process
+of creating a new GSA key and updating the GitHub secret.
+
+## Prerequisites
+
+- Access to the Google Cloud Console for the relevant project
+- Admin access to the GitHub repository to update secrets
+- Knowledge of which Google Service Account is used for the trivy-scanner workflow
+
+## Creating a New GSA Key in Google Cloud Console
+
+1. **Navigate to the Google Cloud Console**
+   - Go to https://console.cloud.google.com
+   - Select the appropriate project (e.g., `hail-vdc`)
+
+2. **Open the Service Accounts page**
+   - In the left navigation menu, go to **IAM & Admin** → **Service Accounts**
+   - Or navigate directly to: https://console.cloud.google.com/iam-admin/serviceaccounts
+
+3. **Find the Service Account**
+   - Locate the `trivy-scanner` service account.
+   - Click on the service account name to open its details page
+
+4. **Create a New Key**
+   - Click on the **KEYS** tab
+   - Click **ADD KEY** → **Create new key**
+   - Select **JSON** as the key type
+   - Click **CREATE**
+   - The JSON key file will automatically download to your computer
+
+5. **Save the Key Securely**
+   - The downloaded file contains sensitive credentials
+   - Store it temporarily in a secure location until you've updated the GitHub secret
+
+## Copying the Key to GitHub Secret
+
+1. **Open the Key File**
+   - Open the downloaded JSON key file in a text editor
+   - The file contains a JSON object with fields like `type`, `project_id`, `private_key_id`,
+     `private_key`, `client_email`, etc.
+
+2. **Copy the Entire Contents**
+   - Select all contents of the JSON file (the entire JSON object)
+   - Copy it to your clipboard
+   - Ensure you copy the complete JSON, including all opening and closing braces
+
+3. **Navigate to GitHub Repository Settings**
+   - Go to the repository: https://github.com/hail-is/hail
+   - Click on **Settings** (requires admin access)
+   - In the left sidebar, click **Secrets and variables** → **Actions**
+
+4. **Update the Secret**
+   - Find the `GOOGLE_GAR_CREDENTIALS` secret in the list
+   - Click **Update** (or if it doesn't exist, click **New repository secret**)
+   - Paste the entire JSON key contents into the **Secret** field
+   - Click **Update secret** (or **Add secret**)
+   - You might need to authenticate with 2FA to update the secret
+
+5. **Verify the Update**
+   - The secret should now show as "Last updated: now"
+   - You can verify it works by running the Trivy Security Scan workflow manually
+   - Go to **Actions** → **Trivy Security Scan** → **Run workflow**
+
+## Cleanup
+
+After successfully updating the GitHub secret:
+
+1. **Delete the Old Keys**
+   - Return to the Google Cloud Console Service Accounts page
+   - Open the service account's **KEYS** tab
+   - Identify the old key (it will have an older creation date)
+   - Click the **Delete** icon (trash can) next to the old key
+   - Confirm the deletion
+
+2. **Delete the Local Key File**
+   - Securely delete the downloaded JSON key file from your local machine
+   - Consider using `shred` or secure deletion tools if the file contained highly sensitive data
+
+## Troubleshooting
+
+- **Authentication errors in workflow**: Verify the JSON was copied completely and correctly
+- **Permission denied errors**: Ensure the service account has the necessary Artifact Registry permissions
+- **Key not found**: Verify you're using the correct service account for the trivy-scanner workflow
diff --git a/dev-docs/services/docker-hub-cache.md b/dev-docs/services/docker-hub-cache.md
new file mode 100644
index 00000000000..ef392433f8f
--- /dev/null
+++ b/dev-docs/services/docker-hub-cache.md
@@ -0,0 +1,118 @@
+# Docker Hub Cache/Proxy
+
+Hail in GCP provides the option of using a Google Artifact Registry (GAR) remote repository as a proxy/cache for Docker Hub images to mitigate rate limiting issues when pulling images from Docker Hub.
+
+## Overview
+
+When worker VMs or CI/CD processes pull Docker images, they can encounter Docker Hub rate limits, especially when multiple VMs share the same outbound IP (e.g., behind CloudNAT). To address this, we use a GAR set up with a remote origin targeting Docker Hub, that acts as a pull-through cache.
+
+### How It Works
+
+1. **GAR Remote Repository**: A Google Artifact Registry repository configured as a remote repository targeting Docker Hub.
+2. **Image Rewriting**: Docker Hub image references are automatically rewritten to use the GAR proxy before pulling.
+3. **Transparent Caching**: The GAR repository caches images on first pull, and subsequent pulls use the cached version, reducing requests to Docker Hub.
+
+## Configuration
+
+### Terraform Setup
+
+The Docker Hub proxy repo is created in Terraform (`infra/gcp/main.tf` and `infra/gcp-broad/main.tf`) as an Artifact Registry repository with the mode set to `REMOTE` and the target set to `DOCKER_HUB`.
+
+Note: By default the repository is configured to pull anonymously from Docker Hub. That setup is very likely to run into the toomanyrequests error from dockerhub because AR, as a global service, reuses the same IP address for multiple requests across multiple users and projects. To avoid this, it is recommended to create a "hail system" docker hub account, create a personal access token, and configure the repository to pull from Docker Hub using that token manually in the google cloud console.
+
+### IAM Permissions
+
+Access to the `dockerhubproxy` repository is granted via a single Terraform IAM binding that uses a `principalSet` to grant `roles/artifactregistry.reader` to all service accounts in the project:
+
+```
+principalSet://cloudresourcemanager.googleapis.com/projects/{project_number}/type/ServiceAccount
+```
+
+This means:
+- All existing service accounts in the project automatically have read access
+- All newly created service accounts automatically have read access
+- No individual permission grants are needed when creating service accounts
+
+### Global Config
+
+A value called `dockerhub_prefix` is stored in the `global-config` Kubernetes secret by Terraform. Its value is the URI prefix for the Docker Hub proxy repository and made available to:
+
+- Batch services via environment variables (`DOCKERHUB_PREFIX`)
+- CI/CD processes via build configuration
+- Makefile targets via the `DOCKERHUB_PREFIX` variable from config.mk
+
+If the `dockerhub_prefix` value is not set, no rewriting is done and images are pulled from Docker Hub directly regardless of the `dockerhub_proxy` feature flag value (see below).
+
+### Feature Flag
+
+There is a feature flag called `dockerhub_proxy` that is stored in the `feature_flags` table in the database. Its value determines whether user job requests are rewritten to use the Docker Hub proxy repository. This allows us to enable or disable the Docker Hub proxy for all user jobs at runtime without having to rebuild the system or manually update global-config.
+
+Because batch instances read the feature flag value only once at startup, switching the feature flag value will not take effect until the batch instances are restarted (eg `kubectl rollout restart deployment batch`).
+
+Note that CI/CD build jobs and makefile targets are independently implemented and do not look at the `dockerhub_proxy` feature flag.
+
+## Image Rewriting
+
+In general, image names in code are still specified in their natural form. Before pulling an image, we update or rewrite the image name to make sure it is pulled from the proxy registry (if configured).
+
+Image names can be specified as:
+
+- Bare images (e.g., `ubuntu:24.04`)
+- Organization images (e.g., `envoyproxy/envoy:v1.33.0`)
+- Registry images (e.g., `us-central1-docker.pkg.dev/my-project/my-repo/my-image:latest`)
+
+The rewriting rules are:
+
+- Bare images are rewritten to `{dockerhub_prefix}/library/{image_name}` (eg `us-central1-docker.pkg.dev/my-project/dockerhubproxy/library/ubuntu:24.04`)
+- Organization images are rewritten to `{dockerhub_prefix}/{organization}/{image_name}` (eg `us-central1-docker.pkg.dev/my-project/dockerhubproxy/envoyproxy/envoy:v1.33.0`)
+- Registry images are not rewritten (eg `us-central1-docker.pkg.dev/my-project/my-repo/my-image:latest`)
+
+### Job Submission
+
+At job submission time, if the `dockerhub_proxy` feature flag is enabled and the global-config `dockerhub_prefix` variable is set, the image name is rewritten to use the `DOCKERHUB_PREFIX` variable.
+
+### CI/CD Processes
+
+Within CI/CD builds, the `DOCKERHUB_PREFIX` variable is automatically set to the `dockerhub_prefix` value from the `global-config` secret.
+
+Each task which interacts with Docker Hub images should apply the rewriting rules to the image name before pulling the image.
+
+- Some examples of CI/CD build tasks which have been updated to use `DOCKERHUB_PREFIX` are:
+  - `copy_third_party_images` in `build.yaml`
+  - `mirror_hailgenetics_images` in `build.yaml`
+
+
+### Makefile Targets
+
+Makefile targets use config.mk to set the `DOCKERHUB_PREFIX` variable. Thereafter if they need to interact with Docker Hub images, they should apply the rewriting rules to the image name before pulling the image. 
+
+
+Note: It's likely that underlying scripts are shared between the CI/CD tasks and the Makefile targets, so the rewriting rules should be applied in the shared script. Then the only responsibility of the Makefile targets is to set the `DOCKERHUB_PREFIX` variable.
+
+Some examples of Makefile targets which have been updated to use `DOCKERHUB_PREFIX`:
+  - `docker/third-party/Makefile` target: `copy`
+  - `docker/hailgenetics/Makefile` target: `mirror-dockerhub-images`
+
+## Usage
+
+### System
+
+The rewriting rules are applied to the image name before pulling the image in the following contexts:
+
+- **Batch services (user jobs)**: At job submission time, if both `DOCKERHUB_PREFIX` is set and the `dockerhub_proxy` feature flag is enabled
+- **CI/CD builds**: Automatically if `DOCKERHUB_PREFIX` is set (does not depend on feature flag)
+- **Makefile targets**: Automatically if `DOCKERHUB_PREFIX` is set (does not depend on feature flag)
+
+### Manual Image Pulls
+
+If you need to manually pull an image through the proxy, you can construct the path:
+
+```bash
+# Example: Pulling ubuntu:24.04 through the proxy
+REGION=us-central1
+PROJECT=your-project
+IMAGE=ubuntu:24.04
+docker pull ${REGION}-docker.pkg.dev/${PROJECT}/dockerhubproxy/library/${IMAGE}
+```
+
+Note that from your local machine you will need to make sure you have logged in to gcloud as a user who is allowed to access the `dockerhubproxy` repository. You must also run `gcloud auth configure-docker` to configure docker to use your gcloud credentials when making docker pull calls.
diff --git a/dev-docs/services/tls.md b/dev-docs/services/tls.md
index d9a212fec43..109ad9f5c5e 100644
--- a/dev-docs/services/tls.md
+++ b/dev-docs/services/tls.md
@@ -13,7 +13,6 @@ communications between it and the outside world.
 Currently, all traffic in our cluster should be encrypted except for:
 - from the batch-driver to the batch workers
 - from the batch workers to the internal-gateway
-- to ukbb-rg
 - from the notebook service to the notebook workers
 - to letsencrypt (oh the irony)
 
diff --git a/devbin/dev_proxy.py b/devbin/dev_proxy.py
index bfa0ab7d453..b9972200773 100644
--- a/devbin/dev_proxy.py
+++ b/devbin/dev_proxy.py
@@ -5,7 +5,7 @@
 from hailtop.auth import hail_credentials
 from hailtop.aiocloud.common import Session
 
-from web_common import render_template, setup_aiohttp_jinja2, setup_common_static_routes
+from web_common import render_template, setup_aiohttp_jinja2, setup_common_static_routes, web_security_headers
 
 from aiohttp import web
 import aiohttp_session
@@ -23,11 +23,13 @@
 
 
 @routes.view('/api/{route:.*}')
+@web_security_headers
 async def default_proxied_api_route(request: web.Request):
     return web.json_response(await proxy(request))
 
 
 @routes.view('/{route:.*}')
+@web_security_headers
 async def default_proxied_web_route(request: web.Request):
     return await render_html(request, await proxy(request))
 
diff --git a/docker/copy_image.sh b/docker/copy_image.sh
index c14b2c331ab..b7bc809a066 100755
--- a/docker/copy_image.sh
+++ b/docker/copy_image.sh
@@ -1,7 +1,27 @@
 if command -v skopeo
 then
     copy_image() {
-        skopeo copy --override-os linux --override-arch amd64 docker://docker.io/$1 docker://$2
+        src=$1
+        # Check if source already has a registry prefix
+        # A registry is indicated by the first part (before first '/') containing a '.' or ':'
+        # Examples: "docker.io/ubuntu", "us-central1-docker.pkg.dev/...", "localhost:5000/image"
+        if [[ "$src" == *"/"* ]]
+        then
+            # Extract the first part (registry/namespace)
+            first_part="${src%%/*}"
+            # If first part contains '.' or ':', it's a registry
+            if [[ "$first_part" == *"."* ]] || [[ "$first_part" == *":"* ]]
+            then
+                # Source already has a registry prefix (e.g., "us-central1-docker.pkg.dev/.../library/ubuntu:24.04")
+                skopeo copy --override-os linux --override-arch amd64 docker://$src docker://$2
+            else
+                # First part is just a namespace (e.g., "envoyproxy/envoy:v1.33.0"), prepend docker.io/
+                skopeo copy --override-os linux --override-arch amd64 docker://docker.io/$src docker://$2
+            fi
+        else
+            # Bare image name (e.g., "ubuntu:24.04"), prepend docker.io/
+            skopeo copy --override-os linux --override-arch amd64 docker://docker.io/$src docker://$2
+        fi
     }
 else
     echo Could not find skopeo, falling back to docker which will be slower.
diff --git a/docker/hail-ubuntu/Dockerfile b/docker/hail-ubuntu/Dockerfile
index 95482abea4b..92a0d02318e 100644
--- a/docker/hail-ubuntu/Dockerfile
+++ b/docker/hail-ubuntu/Dockerfile
@@ -1,6 +1,6 @@
 ARG DOCKER_PREFIX={{ global.docker_prefix }}
 ARG SKIP_GCLOUD_PROFILER=false
-FROM $DOCKER_PREFIX/ubuntu:noble-20251013 AS initializer
+FROM $DOCKER_PREFIX/ubuntu:noble-20260113 AS initializer
 
 ENV LANG=C.UTF-8
 ENV DEBIAN_FRONTEND=noninteractive
diff --git a/docker/hailgenetics/Makefile b/docker/hailgenetics/Makefile
index 97cff8c8d3d..8f99e6a756f 100644
--- a/docker/hailgenetics/Makefile
+++ b/docker/hailgenetics/Makefile
@@ -7,5 +7,6 @@ publish-python-dill:
 
 mirror-dockerhub-images:
 	DOCKER_PREFIX=$(DOCKER_PREFIX) \
+	DOCKERHUB_PREFIX=$(DOCKERHUB_PREFIX) \
 	HAIL_PIP_VERSION=$(shell cat ../../hail/env/HAIL_PIP_VERSION) \
 	./mirror_images.sh
diff --git a/docker/hailgenetics/mirror_images.sh b/docker/hailgenetics/mirror_images.sh
index 67a00f4db38..8a44d35099a 100755
--- a/docker/hailgenetics/mirror_images.sh
+++ b/docker/hailgenetics/mirror_images.sh
@@ -7,12 +7,30 @@ source ../copy_image.sh
 copy_if_not_present() {
     src_image=$1
     dest_image=$2
-    if ! skopeo inspect "docker://docker.io/$1";
+    # If DOCKERHUB_PREFIX is set, prepend it to the source image
+    if [ -n "${DOCKERHUB_PREFIX}" ]
     then
-        echo "$1 does not exist yet, doing nothing"
+        # Image is already namespaced (e.g., "hailgenetics/python-dill:3.10")
+        src="${DOCKERHUB_PREFIX}/${src_image}"
     else
-      echo "copying $1 to $2"
-      copy_image $1 $2
+        # No dockerhub prefix, use docker.io as before
+        src="$src_image"
+    fi
+    
+    # Check if image exists (using docker.io for the check if no prefix, otherwise use the prefixed source)
+    if [ -n "${DOCKERHUB_PREFIX}" ]
+    then
+        check_src="$src"
+    else
+        check_src="docker.io/$src_image"
+    fi
+    
+    if ! skopeo inspect "docker://${check_src}";
+    then
+        echo "$src_image does not exist yet, doing nothing"
+    else
+      echo "copying $src_image to $dest_image"
+      copy_image "$src" "$dest_image"
     fi
 }
 
diff --git a/docker/third-party/Makefile b/docker/third-party/Makefile
index a2ab3de264f..fd68a8257c7 100644
--- a/docker/third-party/Makefile
+++ b/docker/third-party/Makefile
@@ -2,4 +2,4 @@ include ../../config.mk
 
 .PHONY: copy
 copy:
-	DOCKER_PREFIX=$(DOCKER_PREFIX) bash copy_images.sh
+	DOCKER_PREFIX=$(DOCKER_PREFIX) DOCKERHUB_PREFIX=$(DOCKERHUB_PREFIX) bash copy_images.sh
diff --git a/docker/third-party/copy_images.sh b/docker/third-party/copy_images.sh
index f890d721470..7f856fa3895 100755
--- a/docker/third-party/copy_images.sh
+++ b/docker/third-party/copy_images.sh
@@ -15,5 +15,22 @@ fi
 for image in ${images}
 do
     dest="${DOCKER_PREFIX}/${image}"
-    copy_image $image $dest
+    # If DOCKERHUB_PREFIX is set, prepend it to the source image
+    if [ -n "${DOCKERHUB_PREFIX}" ]
+    then
+        # Handle both bare images (e.g., "ubuntu") and namespaced images (e.g., "envoyproxy/envoy:v1.33.0")
+        # For bare images, we need to add "library/" prefix
+        if [[ "$image" == *"/"* ]]
+        then
+            # Already namespaced (e.g., "envoyproxy/envoy:v1.33.0")
+            src="${DOCKERHUB_PREFIX}/${image}"
+        else
+            # Bare image (e.g., "ubuntu"), need to add "library/" prefix
+            src="${DOCKERHUB_PREFIX}/library/${image}"
+        fi
+    else
+        # No dockerhub prefix, use docker.io as before
+        src="$image"
+    fi
+    copy_image "$src" "$dest"
 done
diff --git a/docker/third-party/images.txt b/docker/third-party/images.txt
index 5fdf87e2f28..fe1f8a5227d 100644
--- a/docker/third-party/images.txt
+++ b/docker/third-party/images.txt
@@ -19,4 +19,4 @@ ubuntu:18.04
 ubuntu:20.04
 ubuntu:22.04
 ubuntu:24.04
-ubuntu:noble-20251013
+ubuntu:noble-20260113
\ No newline at end of file
diff --git a/gear/pinned-requirements.txt b/gear/pinned-requirements.txt
index 033f00d6feb..5fcdb908e67 100644
--- a/gear/pinned-requirements.txt
+++ b/gear/pinned-requirements.txt
@@ -6,7 +6,7 @@ aiohappyeyeballs==2.6.1
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
@@ -35,24 +35,30 @@ attrs==25.4.0
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
-cachetools==6.2.2
+certifi==2026.1.4
     # via
+    #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
-    #   google-auth
-certifi==2025.11.12
+    #   kubernetes-asyncio
+    #   requests
+cffi==2.0.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
-    #   kubernetes-asyncio
-    #   requests
+    #   cryptography
 charset-normalizer==3.4.4
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   requests
+cryptography==46.0.5
+    # via
+    #   -c gear/../hail/python/hailtop/pinned-requirements.txt
+    #   -c gear/../hail/python/pinned-requirements.txt
+    #   google-auth
 frozenlist==1.8.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
@@ -60,11 +66,11 @@ frozenlist==1.8.0
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   aiosignal
-google-api-core==2.28.1
+google-api-core==2.30.0
     # via google-api-python-client
-google-api-python-client==2.187.0
+google-api-python-client==2.190.0
     # via google-cloud-profiler
-google-auth==2.43.0
+google-auth==2.48.0
     # via
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
@@ -72,7 +78,7 @@ google-auth==2.43.0
     #   google-api-python-client
     #   google-auth-httplib2
     #   google-cloud-profiler
-google-auth-httplib2==0.2.1
+google-auth-httplib2==0.3.0
     # via
     #   google-api-python-client
     #   google-cloud-profiler
@@ -80,7 +86,7 @@ google-cloud-profiler==4.1.0
     # via -r gear/requirements.txt
 googleapis-common-protos==1.72.0
     # via google-api-core
-httplib2==0.31.0
+httplib2==0.31.2
     # via
     #   google-api-python-client
     #   google-auth-httplib2
@@ -93,21 +99,21 @@ idna==3.11
     #   yarl
 kubernetes-asyncio==19.15.1
     # via -r gear/requirements.txt
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   yarl
-packaging==25.0
+packaging==26.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   -r gear/requirements.txt
 prometheus-async==19.2.0
     # via -r gear/requirements.txt
-prometheus-client==0.23.1
+prometheus-client==0.24.1
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -r gear/requirements.txt
@@ -119,15 +125,15 @@ propcache==0.4.1
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiohttp
     #   yarl
-proto-plus==1.26.1
+proto-plus==1.27.1
     # via google-api-core
-protobuf==6.33.1
+protobuf==6.33.5
     # via
     #   google-api-core
     #   google-cloud-profiler
     #   googleapis-common-protos
     #   proto-plus
-pyasn1==0.6.1
+pyasn1==0.6.2
     # via
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
@@ -138,11 +144,17 @@ pyasn1-modules==0.4.2
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   google-auth
+pycparser==3.0
+    # via
+    #   -c gear/../hail/python/dev/pinned-requirements.txt
+    #   -c gear/../hail/python/hailtop/pinned-requirements.txt
+    #   -c gear/../hail/python/pinned-requirements.txt
+    #   cffi
 pymysql==1.1.2
     # via
     #   -r gear/requirements.txt
     #   aiomysql
-pyparsing==3.2.5
+pyparsing==3.3.2
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   httplib2
@@ -170,9 +182,11 @@ rsa==4.9.1
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   google-auth
-setuptools==80.9.0
+setuptools==81.0.0
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
+    #   -c gear/../hail/python/hailtop/pinned-requirements.txt
+    #   -c gear/../hail/python/pinned-requirements.txt
     #   kubernetes-asyncio
 six==1.17.0
     # via
@@ -192,10 +206,11 @@ typing-extensions==4.15.0
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
     #   -c gear/../hail/python/pinned-requirements.txt
     #   aiosignal
+    #   cryptography
     #   multidict
 uritemplate==4.2.0
     # via google-api-python-client
-urllib3==2.5.0
+urllib3==2.6.3
     # via
     #   -c gear/../hail/python/dev/pinned-requirements.txt
     #   -c gear/../hail/python/hailtop/pinned-requirements.txt
diff --git a/hail/.gitignore b/hail/.gitignore
index d72c8184c41..186f5ce05e7 100644
--- a/hail/.gitignore
+++ b/hail/.gitignore
@@ -73,7 +73,6 @@ src/main/c/.cxx.vsn
 src/main/c/headers
 src/main/c/lib
 src/main/c/libsimdpp-2*
-src/main/resources/build-info.properties
 src/main/resources/include/catch.hpp
 env/
 www/docs
diff --git a/hail/.scalafix.conf b/hail/.scalafix.conf
index cc8cb91078d..dab76d2e8d0 100644
--- a/hail/.scalafix.conf
+++ b/hail/.scalafix.conf
@@ -31,5 +31,6 @@ RemoveUnused {
 }
 
 ForbiddenSymbol.symbols = [
-  "scala.collection.compat.immutable.ArraySeq"
+  "scala.collection.mutable.AnyRefMap",
+  "scala.collection.compat.immutable.ArraySeq",
 ]
diff --git a/hail/build.mill b/hail/build.mill
index b27546b8c91..3d0946c48c5 100644
--- a/hail/build.mill
+++ b/hail/build.mill
@@ -1,439 +1,143 @@
 //| mill-version: 1.0.4
 //| mill-jvm-version: 11
-
 package build
 
-import com.goyeau.mill.scalafix.ScalafixModule
 import mill.*
-import mill.api.{BuildCtx, Result}
+import mill.api.Result
 import mill.scalalib.*
-import mill.scalalib.Assembly.*
-import mill.scalalib.TestModule.TestNg
 import mill.scalalib.scalafmt.ScalafmtModule
-import mill.util.{Jvm, VcsVersion}
+
+import millbuild.BuildConfig.*
+import millbuild.BuildMode.*
+import millbuild.MvnCoordinate.*
+
+import com.goyeau.mill.scalafix.ScalafixModule
 import org.typelevel.scalacoptions.*
-import upickle.default.ReadWriter
 
-object Settings {
+object Settings:
   val hailMajorMinorVersion = "0.2"
   val hailPatchVersion = "137"
   val scalaMinorVersions = Map("2.12" -> "2.12.20", "2.12.13" -> "2.12.13", "2.13" -> "2.13.13")
-}
 
-object Deps {
 
-  object Asm {
-    val `asm-bom` = mvn"org.ow2.asm:asm-bom:9.9"
-    val asm = mvn"org.ow2.asm:asm"
-    val `asm-analysis` = mvn"org.ow2.asm:asm-analysis"
-    val `asm-util` = mvn"org.ow2.asm:asm-util"
-  }
-
-  object Breeze {
-    // WARNING WARNING WARNING
-    // Before changing the breeze version review:
-    // - https://hail.zulipchat.com/#narrow/stream/123011-Hail-Query-Dev/topic/new.20spark.20ndarray.20failures/near/41645
-    // - https://github.com/hail-is/hail/pull/11555
-    val breeze = mvn"org.scalanlp::breeze:1.1"
-    val `breeze-natives` = mvn"org.scalanlp::breeze-natives:1.1"
-  }
-
-  object GoogleCloud {
-    val `libraries-bom` = mvn"com.google.cloud:libraries-bom:26.66.0"
-    val `google-auth-library-oauth2-http` = mvn"com.google.auth:google-auth-library-oauth2-http"
-    val `google-cloud-storage` = mvn"com.google.cloud:google-cloud-storage"
-  }
-
-  object Spark {
-    def core: Task[Dep] = Task.Anon(mvn"org.apache.spark::spark-core:${Env.sparkVersion()}")
-    def mllib: Task[Dep] = Task.Anon(mvn"org.apache.spark::spark-mllib:${Env.sparkVersion()}")
-
-    // direct dependencies provided by Spark at runtime
-    val avro = mvn"org.apache.avro:avro:1.11.2"
-    val `commons-codec` = mvn"commons-codec:commons-codec:1.16.1"
-    val `commons-io` = mvn"commons-io:commons-io:2.16.1"
-    val `commons-lang3` = mvn"org.apache.commons:commons-lang3:3.12.0"
-    val `commons-math3` = mvn"org.apache.commons:commons-math3:3.6.1"
-    val `hadoop-client-api` = mvn"org.apache.hadoop:hadoop-client-api:3.3.4"
-    val httpclient = mvn"org.apache.httpcomponents:httpclient:4.5.14"
-    val `jackson-core` = mvn"com.fasterxml.jackson.core:jackson-core:2.15.2"
-    val `json4s-jackson` = mvn"org.json4s::json4s-jackson:3.7.0-M11"
-    val `l4z-java` = mvn"org.lz4:lz4-java:1.8.0"
-    val `log4j-bom` = mvn"org.apache.logging.log4j:log4j-bom:2.22.0"
-    val `logj4-api` = mvn"org.apache.logging.log4j:log4j-api"
-    val `log4j-core` = mvn"org.apache.logging.log4j:log4j-core"
-    val `zstd-jni` = mvn"com.github.luben:zstd-jni:1.5.5-4"
-  }
+object Env extends Module:
+  def sparkVersion: T[String] =
+    Task.Input {
+      Task.env.getOrElse("SPARK_VERSION", "3.5.3")
+    }
 
-  val `elasticsearch-spark` = mvn"org.elasticsearch::elasticsearch-spark-30:9.2.1"
-  val freemarker = mvn"org.freemarker:freemarker:2.3.31"
-  val htsjdk = mvn"com.github.samtools:htsjdk:3.0.5"
-  val jdistlib = mvn"net.sourceforge.jdistlib:jdistlib:0.4.5"
-  val jna = mvn"net.java.dev.jna:jna:5.13.0"
-  val `junixsocket-core` = mvn"com.kohlschutter.junixsocket:junixsocket-core:2.6.1"
-  val `log4j-api-scala` = mvn"org.apache.logging.log4j::log4j-api-scala:13.1.0"
-  val netlib = mvn"com.github.fommil.netlib:all:1.1.2"
-  val `scala-collection-compat` = mvn"org.scala-lang.modules::scala-collection-compat:2.13.0"
-  // provides @nowarn212 and @nowarn213
-  val `scalac-compat-annotation` = mvn"org.typelevel::scalac-compat-annotation:0.1.4"
-  val sourcecode = mvn"com.lihaoyi::sourcecode:0.4.2"
 
-  object Plugins {
-    val `better-monadic-for` = mvn"com.olegpy::better-monadic-for:0.3.1"
-  }
-}
+trait HailJavaModule extends JavaModule:
+  override def javacOptions: T[Seq[String]] = {
+    val `java-1.8` =
+      if System.getProperty("java.version").startsWith("1.8")
+      then Seq("-Xlint:-processing")
+      else Seq()
 
-enum BuildMode derives ReadWriter {
-  case dev, ci, release
-}
+    val `optim?` =
+      if buildMode == Release
+      then Seq("-O")
+      else Seq("-g")
 
-object Env extends Module {
-  def javaVersion: T[String] = Task.Input {
-    System.getProperty("java.version")
-  }
-
-  def sparkVersion: T[String] = Task.Input {
-    Result.Success(Task.env.getOrElse("SPARK_VERSION", "3.5.3"))
+    `java-1.8` ++ `optim?` ++ Seq(
+      "-Xlint:all",
+      "-Werror",
+    )
   }
 
-  val buildMode: BuildMode = BuildMode.valueOf(millbuild.BuildConfig.buildMode)
-}
-
-trait HailModule extends ScalaModule with ScalafmtModule with ScalafixModule { outer =>
-  // crossValue is defined by the RootHailModule#CrossValue trait, which this will be mixed with.
-  // It propagates the cross value from the root `hail` module.
-  def crossValue: String
-  override def scalaVersion: T[String] = Task { Settings.scalaMinorVersions(crossValue) }
 
-  override def scalafixIvyDeps: T[Seq[Dep]] = Seq(
-    mvn"io.github.tanin47::scalafix-forbidden-symbol:1.0.0",
-  )
+trait HailScalaModule extends ScalaModule, HailJavaModule, ScalafmtModule, ScalafixModule:
+  outer =>
 
-  override def depManagement: T[Seq[Dep]] =
+  override def scalafixIvyDeps: T[Seq[Dep]] =
     Seq(
-      Deps.`scala-collection-compat`,
-    )
-
-  override def javacOptions: T[Seq[String]] = Seq(
-    "-Xlint:all",
-    "-Werror",
-    if (Env.buildMode == BuildMode.release) "-O" else "-g",
-  ) ++ (if (!Env.javaVersion().startsWith("1.8")) Seq("-Xlint:-processing") else Seq())
-
-  override def scalacOptions: T[Seq[String]] = Task {
-    val disabledOptions = Set(
-      ScalacOptions.warnUnusedParams, ScalacOptions.privateWarnUnusedParams,
-      ScalacOptions.warnUnusedImplicits, ScalacOptions.privateWarnUnusedImplicits,
-      ScalacOptions.warnUnusedExplicits,
-      // we don't enable the unused imports warning in 2.12, as the wconf origin filter doesn't work
-      ScalacOptions.privateWarnUnusedImports,
-      // 2.13 added the -Wnonunit-discard flag, which is a stronger check than -Wvalue-discard
-      ScalacOptions.warnValueDiscard, ScalacOptions.privateWarnValueDiscard,
-
-      ScalacOptions.lintInferAny,
-      ScalacOptions.languageExperimentalMacros,
+      `scalafix-forbidden-symbol` :: "1.0.0",
     )
-    
-    val baseOptions = ScalacOptions.default +
-      ScalacOptions.source213 +
-      ScalacOptions.advancedOption("no-patmat-analysis")
-    
-    val additionalOptions = Env.buildMode match {
-      case BuildMode.`dev` =>
-        ScalacOptions.verboseOptions
-      // enable to help debug accessing unitialized fields
-      //     + ScalacOptions.checkInit
-      case BuildMode.`ci` =>
-        Set(ScalacOptions.fatalWarnings)
-      case BuildMode.`release` =>
-        Set(
-          ScalacOptions.fatalWarnings,
-          ScalacOptions.optimizerMethodLocal,
-          ScalacOptions.optimizerOption(":-closure-invocations"),
-        )
-    }
 
-    val finalOptions = ScalacOptions.tokensForVersion(
-      ScalaVersion.unsafeFromString(scalaVersion()),
-      baseOptions -- disabledOptions ++ additionalOptions
-    )
-    if (scalaVersion().startsWith("2.13")) {
-      finalOptions ++
-      Seq(
-       // collection types
-        // value ArrayStack in package mutable is deprecated (since 2.13.0): Use Stack instead of ArrayStack; it now uses an array-based implementation
-        "-Wconf:cat=deprecation&msg=value ArrayStack in package mutable is deprecated:s",
-      // generic to immutable default
-      // collection methods
-        // method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated (since 2.13.0): implicit conversions from Array to immutable.IndexedSeq are implemented by copying; use `toIndexedSeq` explicitly if you want to copy, or use the more efficient non-copying ArraySeq.unsafeWrapArray
-        "-Wconf:cat=deprecation&msg=method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated:s",
-        // Passing an explicit array value to a Scala varargs method is deprecated (since 2.13.0) and will result in a defensive copy; Use the more efficient non-copying ArraySeq.unsafeWrapArray or an explicit toIndexedSeq call
-        "-Wconf:cat=deprecation&msg=Passing an explicit array value to a Scala varargs method is deprecated:s",
-        // method any2stringadd in object Predef is deprecated (since 2.13.0): Implicit injection of + is deprecated. Convert to String to call +
-        "-Wconf:cat=deprecation&msg=any2stringadd:s",
-        // method + in class Char is deprecated (since 2.13.0): Adding a number and a String is deprecated. Use the string interpolation `s"$num$str"`
-        raw"-Wconf:cat=deprecation&msg=method \+ in class Char is deprecated:s",
-        // method toIterable in trait Iterable is deprecated (since 2.13.7): toIterable is internal and will be made protected; its name is similar to `toList` or `toSeq`, but it doesn't copy non-immutable collections
-        "-Wconf:cat=deprecation&msg=method toIterable in trait Iterable is deprecated:s",
-        // method toIterator in class IterableOnceExtensionMethods is deprecated (since 2.13.0): Use .iterator instead
-        "-Wconf:cat=deprecation&msg=toIterator:s",
-        // method foreach in class IterableOnceExtensionMethods is deprecated (since 2.13.0): Use .iterator.foreach(...) instead
-        "-Wconf:cat=deprecation&msg=foreach:s",
-        // method nonEmpty in class IterableOnceExtensionMethods is deprecated (since 2.13.0): Use .iterator.nonEmpty instead
-        "-Wconf:cat=deprecation&msg=method nonEmpty in class IterableOnceExtensionMethods is deprecated:s",
-        // method view in trait IndexedSeqOps is deprecated (since 2.13.0): Use .view.slice(from, until) instead of .view(from, until)
-        "-Wconf:cat=deprecation&msg=method view in trait IndexedSeqOps is deprecated:s",
-        // method reverseContents in class StringBuilder is deprecated (since 2.13.0): Use reverseInPlace instead
-        "-Wconf:cat=deprecation&msg=method reverseContents in class StringBuilder is deprecated:s",
-        // method + in trait MapOps is deprecated (since 2.13.0): Consider requiring an immutable Map or fall back to Map.concat.
-        raw"-Wconf:cat=deprecation&msg=method \+ in trait MapOps is deprecated:s",
-        "-Wconf:cat=deprecation&msg=method - in trait MapOps is deprecated:s",
-        // method mapValues in trait MapOps is deprecated (since 2.13.0): Use .view.mapValues(f). A future version will include a strict version of this method (for now, .view.mapValues(f).toMap).
-        "-Wconf:cat=deprecation&msg=method mapValues in trait MapOps is deprecated:s",
-        // method filterKeys in trait MapOps is deprecated (since 2.13.0): Use .view.filterKeys(f). A future version will include a strict version of this method (for now, .view.filterKeys(p).toMap).
-        "-Wconf:cat=deprecation&msg=method filterKeys in trait MapOps is deprecated:s",
-        // method - in trait SetOps is deprecated (since 2.13.0): Consider requiring an immutable Set or fall back to Set.diff
-        "-Wconf:cat=deprecation&msg=method - in trait SetOps is deprecated:s",
-        // method reverseMap in trait SeqOps is deprecated (since 2.13.0): Use .reverseIterator.map(f).to(...) instead of .reverseMap(f)
-        "-Wconf:cat=deprecation&msg=method reverseMap in trait SeqOps is deprecated:s",
-        // method transform in trait SeqOps is deprecated (since 2.13.0): Use `mapInPlace` on an `IndexedSeq` instead
-        "-Wconf:cat=deprecation&msg=method transform in trait SeqOps is deprecated:s",
-      // other
-        // Widening conversion from Long to Double is deprecated because it loses precision. Write `.toDouble` instead.
-        "-Wconf:cat=deprecation&msg=Widening conversion from Long to Double:s",
-        "-Wconf:cat=deprecation&msg=symbol literal is deprecated:s",
-        raw"-Wconf:cat=unused-imports&origin=scala\.collection\.compat\._:s",
-        raw"-Wconf:cat=unused-imports&origin=scala\.Option\.option2Iterable:s",
-        raw"-Wconf:cat=unused-imports&origin=is\.hail\.utils\.compat\._:s",
-        raw"-Wconf:msg=unused value of type org\.scalatest\..*Assertion:s",
-        raw"-Wconf:msg=unused value of type org\.mockito\.stubbing\.ScalaOngoingStubbing:s",
-      )
-    } else {
-      finalOptions :+ "-Wconf:msg=legacy-binding:s"
-    }
-  }
-}
-
-object hail extends Cross[RootHailModule](millbuild.BuildConfig.enabledScalaVersions)
-
-trait RootHailModule extends CrossScalaModule with HailModule { outer =>
-  def buildInfo: T[PathRef] = Task {
-    val revision = VcsVersion.vcsState().currentRevision
-    os.write(
-      Task.dest / "build-info.properties",
-      s"""[Build Metadata]
-         |revision=$revision
-         |sparkVersion=${Env.sparkVersion()}
-         |hailPipVersion=${Settings.hailMajorMinorVersion}.${Settings.hailPatchVersion}
-         |hailBuildConfiguration=${Env.buildMode}
-         |""".stripMargin,
+  override def depManagement: T[Seq[Dep]] =
+    Seq(
+      `scala-collection-compat` :: "2.13.0",
     )
-    PathRef(Task.dest)
-  }
-
-  override def moduleDeps: Seq[JavaModule] = Seq(memory)
-
-  override def resources: T[Seq[PathRef]] = super.resources() ++ Seq(
-    BuildCtx.withFilesystemCheckerDisabled {
-      PathRef(BuildCtx.workspaceRoot / "prebuilt" / "lib")
-    },
-    buildInfo(),
-  )
-
-  override def generatedSources: T[Seq[PathRef]] = Task {
-    Seq(`ir-gen`.generate())
-  }
-
-  override def unmanagedClasspath: T[Seq[PathRef]] =
-    Seq(shadedazure.assembly())
-
-  // omit unmanagedClasspath from the jar
-  override def jar: T[PathRef] = Task {
-    val jar = Task.dest / "out.jar"
-    Jvm.createJar(jar, (resources() ++ Seq(compile().classes)).map(_.path).filter(os.exists), manifest())
-    PathRef(jar)
-  }
-
-  override def bomMvnDeps: T[Seq[Dep]] = Seq(
-    Deps.Asm.`asm-bom`,
-    Deps.GoogleCloud.`libraries-bom`,
-    Deps.Spark.`log4j-bom`,
-  )
-
-  override def mvnDeps: T[Seq[Dep]] = Seq(
-    Deps.Asm.asm,
-    Deps.Asm.`asm-analysis`,
-    Deps.Asm.`asm-util`,
-    Deps.GoogleCloud.`google-auth-library-oauth2-http`
-      .excludeOrg(
-        "commons-codec",
-        "org.apache.httpcomponents",
-        "org.slf4j",
-      ),
-    Deps.GoogleCloud.`google-cloud-storage`
-      .excludeOrg(
-        "com.fasterxml.jackson.core",
-        "commons-codec",
-        "org.slf4j",
-      ),
-    Deps.`elasticsearch-spark`
-      .excludeOrg(
-        "commons-logging",
-        "org.apache.spark",
-        "org.slf4j",
-      ),
-    Deps.freemarker,
-    Deps.htsjdk.excludeOrg("*"),
-    Deps.jdistlib.excludeOrg("*"),
-    Deps.`log4j-api-scala`.excludeOrg("*"),
-    Deps.jna,
-    Deps.`scala-collection-compat`,
-    Deps.sourcecode,
-  )
 
-  override def runMvnDeps: T[Seq[Dep]] = Seq(
-    Deps.Breeze.`breeze-natives`
-      .excludeOrg(
-        "org.apache.commons",
-        "org.slf4j",
-      ),
-    Deps.netlib,
-    Deps.`junixsocket-core`,
+  def scalacPluginMvnDeps = Seq(
+    mvn"org.wartremover::wartremover:3.4.1",
+    mvn"org.wartremover::wartremover-contrib:2.3.5",
   )
 
-  override def compileMvnDeps: T[Seq[Dep]] = Seq(
-    Deps.Breeze.breeze,
-    Deps.Spark.core().excludeOrg("org.scalanlp"),  // Hail has an explicit dependency on Breeze 1.1
-    Deps.Spark.mllib().excludeOrg("org.scalanlp"),  // Hail has an explicit dependency on Breeze 1.1
-    Deps.Spark.avro,
-    Deps.Spark.`commons-codec`,
-    Deps.Spark.`commons-io`,
-    Deps.Spark.`commons-lang3`,
-    Deps.Spark.`commons-math3`,
-    Deps.Spark.httpclient,
-    Deps.Spark.`hadoop-client-api`,
-    Deps.Spark.`jackson-core`,
-    Deps.Spark.`json4s-jackson`,
-    Deps.Spark.`l4z-java`,
-    Deps.Spark.`logj4-api`,
-    Deps.Spark.`log4j-core`,
-    Deps.Spark.`zstd-jni`,
-    Deps.`scalac-compat-annotation`,
-  )
-
-  override def assemblyRules: Seq[Rule] = super.assemblyRules ++ Seq(
-    Rule.Exclude("META-INF/INDEX.LIST"),
-    Rule.ExcludePattern("^scala/(?!collection/compat).*"),
-    Rule.AppendPattern("META-INF/services/.*", "\n"),
-    Rule.Relocate("breeze.**", "is.hail.relocated.@0"),
-    Rule.Relocate("com.google.**", "is.hail.relocated.@0"),
-    Rule.Relocate("scala.collection.compat.**", "is.hail.relocated.@0"),
-  )
-
-  override def scalacPluginMvnDeps: T[Seq[Dep]] = Seq(
-    Deps.Plugins.`better-monadic-for`,
-  )
-
-  def writeRunClasspath: T[PathRef] = Task {
-    os.write(
-      Task.dest / "runClasspath",
-      runClasspath().map(_.path).mkString(":"),
-    )
-    PathRef(Task.dest)
-  }
-
-  object `ir-gen` extends HailModule with DefaultTaskModule with CrossValue {
-    override def defaultTask(): String = "generate"
+  override def scalacOptions: T[Seq[String]] =
+    Task {
+      val scalaVersion = this.scalaVersion()
 
-    override def mvnDeps = Seq(
-      mvn"com.lihaoyi::mainargs:0.7.7",
-      mvn"com.lihaoyi::os-lib:0.10.7",
-      mvn"com.lihaoyi::sourcecode:0.4.2",
-    )
+      val base =
+        ScalacOptions.default +
+          ScalacOptions.source213 +
+          ScalacOptions.advancedOption("no-patmat-analysis")
 
-    def generate: T[PathRef] = Task {
-      runner().run(Args("--path", Task.dest).value)
-      PathRef(Task.dest)
-    }
-  }
-
-  object memory extends JavaModule with CrossValue {
-    override def zincIncrementalCompilation: T[Boolean] = false
+      val disabled =
+        Set(
+          ScalacOptions.warnUnusedParams,
+          ScalacOptions.privateWarnUnusedParams,
+          ScalacOptions.warnUnusedImplicits,
+          ScalacOptions.privateWarnUnusedImplicits,
+          ScalacOptions.warnUnusedExplicits,
+          // we don't enable the unused imports warning in 2.12, as the wconf origin filter doesn't work
+          ScalacOptions.privateWarnUnusedImports,
+          // 2.13 added the -Wnonunit-discard flag, which is a stronger check than -Wvalue-discard
+          ScalacOptions.warnValueDiscard,
+          ScalacOptions.privateWarnValueDiscard,
+          ScalacOptions.lintInferAny,
+          ScalacOptions.languageExperimentalMacros,
+        )
 
-    override def javacOptions: T[Seq[String]] =
-      outer.javacOptions() ++ (
-        if (Env.javaVersion().startsWith("1.8")) Seq(
-          "-XDenableSunApiLintControl",
-          "-Xlint:-sunapi",
+      val fromBuildMode =
+        buildMode match {
+          case Dev =>
+            ScalacOptions.verboseOptions
+  //            + ScalacOptions.checkInit // enable to help debug accessing uninitialized fields
+          case CI =>
+            Set(ScalacOptions.fatalWarnings)
+          case Release =>
+            Set(
+              ScalacOptions.fatalWarnings,
+              ScalacOptions.optimizerMethodLocal,
+              ScalacOptions.optimizerOption(":-closure-invocations"),
+            )
+        }
+
+      val richOptions =
+        ScalacOptions.tokensForVersion(
+          ScalaVersion.unsafeFromString(scalaVersion),
+          base -- disabled ++ fromBuildMode,
+      ) :+ "-P:wartremover:only-warn-traverser:org.wartremover.contrib.warts.MissingOverride"
+      //      :+ "-P:wartremover:only-warn-traverser:org.wartremover.contrib.warts.UnsafeInheritance"
+
+      val rawOptions =
+        if scalaVersion < "2.12" || scalaVersion >= "3"
+        then sys.error(s"scalaVersion must be 2.12 or 2.13. Got '$scalaVersion'.")
+        else if scalaVersion < "2.13"
+        then Seq("-Wconf:msg=legacy-binding:s")
+        else Seq(
+          // collection types
+          // value ArrayStack in package mutable is deprecated (since 2.13.0): Use Stack instead of ArrayStack; it now uses an array-based implementation
+          "-Wconf:cat=deprecation&msg=value ArrayStack in package mutable is deprecated:s",
+          // generic to immutable default
+          // collection methods
+          // method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated (since 2.13.0): implicit conversions from Array to immutable.IndexedSeq are implemented by copying; use `toIndexedSeq` explicitly if you want to copy, or use the more efficient non-copying ArraySeq.unsafeWrapArray
+          "-Wconf:cat=deprecation&msg=method copyArrayToImmutableIndexedSeq in class LowPriorityImplicits2 is deprecated:s",
+          // Passing an explicit array value to a Scala varargs method is deprecated (since 2.13.0) and will result in a defensive copy; Use the more efficient non-copying ArraySeq.unsafeWrapArray or an explicit toIndexedSeq call
+          "-Wconf:cat=deprecation&msg=Passing an explicit array value to a Scala varargs method is deprecated:s",
+          // method transform in trait SeqOps is deprecated (since 2.13.0): Use `mapInPlace` on an `IndexedSeq` instead
+          "-Wconf:cat=deprecation&msg=method transform in trait SeqOps is deprecated:s",
+          // other
+          "-Wconf:cat=deprecation&msg=symbol literal is deprecated:s",
+          raw"-Wconf:cat=unused-imports&origin=scala\.collection\.compat\._:s",
+          raw"-Wconf:cat=unused-imports&origin=scala\.Option\.option2Iterable:s",
+          raw"-Wconf:cat=unused-imports&origin=is\.hail\.collection\.compat\._:s",
+          raw"-Wconf:msg=unused value of type org\.scalatest\..*Assertion:s",
+          raw"-Wconf:msg=unused value of type org\.mockito\.stubbing\.ScalaOngoingStubbing:s",
         )
-        else Seq()
-      )
 
-    override def sources: T[Seq[PathRef]] = Task.Sources {
-      val debugOrRelease = if (Env.buildMode == BuildMode.ci) "debug" else "release"
-      os.sub / debugOrRelease / "src"
+      richOptions ++ rawOptions
     }
-  }
-
-  object test extends ScalaTests with TestNg with ScalafmtModule with ScalafixModule {
-    override def forkArgs: T[Seq[String]] =
-      Seq("-Xss4m", "-Xmx4096M")
-
-    override def scalafixIvyDeps: T[Seq[Dep]] =
-      outer.scalafixIvyDeps()
-
-    override def compileMvnDeps: T[Seq[Dep]] =
-       outer.compileMvnDeps()
-
-    override def mvnDeps: T[Seq[Dep]] =
-      outer.mvnDeps() ++ Seq(
-        mvn"com.google.inject:guice:5.1.0",
-        mvn"org.scalacheck::scalacheck:1.18.1",
-        mvn"org.scalatest::scalatest:3.2.19",
-        mvn"org.scalatest::scalatest-shouldmatchers:3.2.19",
-        mvn"org.scalatestplus::scalacheck-1-18:3.2.19.0",
-        mvn"org.scalatestplus::testng-7-10:3.2.19.0",
-        mvn"org.mockito::mockito-scala:1.17.31",
-      )
-
-    override def runMvnDeps: T[Seq[Dep]] =
-      outer.runMvnDeps()
-
-    override def assemblyRules: Seq[Rule] =
-      outer.assemblyRules
-  }
-
-  object shadedazure extends JavaModule {
-    override def mvnDeps: T[Seq[Dep]] = Seq(
-      mvn"com.azure:azure-storage-blob:12.22.0",
-      mvn"com.azure:azure-core-http-netty:1.13.7",
-      mvn"com.azure:azure-identity:1.8.3",
-    )
-
-    override def assemblyRules: Seq[Rule] = Seq(
-      Rule.ExcludePattern("META-INF/*.RSA"),
-      Rule.ExcludePattern("META-INF/*.SF"),
-      Rule.ExcludePattern("META-INF/*.DSA"),
-      Rule.Relocate("com.azure.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("com.ctc.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("com.fasterxml.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("com.microsoft.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("com.nimbusds.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("com.sun.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("io.netty.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("is.hail.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("net.jcip.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("net.minidev.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("org.apache.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("org.codehaus.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("org.objectweb.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("org.reactivestreams.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("org.slf4j.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("reactor.adapter.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("reactor.core.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("reactor.netty.**", "is.hail.shadedazure.@0"),
-      Rule.Relocate("reactor.util.**", "is.hail.shadedazure.@0"),
-    )
-  }
 
-}
+  trait HailScalaTests extends ScalaTests, HailScalaModule
diff --git a/hail/hail/ir-gen/package.mill b/hail/hail/ir-gen/package.mill
new file mode 100644
index 00000000000..2f5cbbc5fa2
--- /dev/null
+++ b/hail/hail/ir-gen/package.mill
@@ -0,0 +1,28 @@
+package build.hail.`ir-gen`
+
+import mill.{Args, DefaultTaskModule, PathRef, T, Task}
+import mill.scalalib.Dep
+
+import millbuild.MvnCoordinate.*
+
+object `package` extends build.HailScalaModule, DefaultTaskModule:
+
+  override def scalaVersion: T[String] =
+    "2.13.18"
+
+  override def defaultTask(): String =
+    "generate"
+
+  override def mvnDeps: T[Seq[Dep]] =
+    Seq[Dep](
+      `mainargs` :: "0.7.7",
+      `os-lib` :: "0.10.7",
+      `sourcecode` :: "0.4.2",
+      `scala-collection-compat`,
+    )
+
+  def generate: T[PathRef] =
+    Task {
+      runner().run(Args("--path", Task.dest).value)
+      PathRef(Task.dest)
+    }
\ No newline at end of file
diff --git a/hail/hail/ir-gen/src/Main.scala b/hail/hail/ir-gen/src/Main.scala
index 6dc7537f620..488c0030a28 100644
--- a/hail/hail/ir-gen/src/Main.scala
+++ b/hail/hail/ir-gen/src/Main.scala
@@ -25,7 +25,7 @@ trait IRDSL {
   protected def oneOrMore[T](x: Type[T]): Type[Seq[T]]
   protected def optional[T](x: Type[T]): Type[Option[T]]
 
-  def name: Type[Name] = att("Name").asInstanceOf[Type[Name]]
+  final def name: Type[Name] = att("Name").asInstanceOf[Type[Name]]
   def child: Type[Child]
   def tableChild: Type[Child]
   def matrixChild: Type[Child]
@@ -81,10 +81,10 @@ trait IRDSL {
 
   // Implicits for common names
 
-  implicit def nameDefaultName(t: Type[Name]): Declaration[Name] =
+  implicit final def nameDefaultName(t: Type[Name]): Declaration[Name] =
     in("name", t)
 
-  implicit def childDefaultName(t: Type[Child]): Declaration[Child] =
+  implicit final def childDefaultName(t: Type[Child]): Declaration[Child] =
     in("child", t)
 }
 
@@ -192,7 +192,7 @@ object IRDSL_Impl extends IRDSL {
 
     override def copyWithNewChildren(newChildren: SeqRepr[Child]): Repr[Child] = {
       assert(newChildren.hasStaticLen(1))
-      ChildRepr(typ, newChildren(0) + s".asInstanceOf[$typ]")
+      ChildRepr(typ, s"${newChildren(0)}.asInstanceOf[$typ]")
     }
   }
 
@@ -247,7 +247,7 @@ object IRDSL_Impl extends IRDSL {
         case (SeqRepr.Static(Seq(), _), r) => r
         case (l, SeqRepr.Static(Seq(), _)) => l
         case (SeqRepr.Static(l, t), SeqRepr.Static(r, _)) => SeqRepr.Static(l ++ r, t)
-        case _ => SeqRepr.Dynamic(this + " ++ " + other, eltType)
+        case _ => SeqRepr.Dynamic(s"$this ++ $other", eltType)
       }
     }
 
@@ -558,7 +558,7 @@ object IRDSL_Impl extends IRDSL {
       s"object $name extends ${name}CompanionExt\n"
     else ""
 
-    def generateDef: String = companionDef + classDef + "\n"
+    override def generateDef: String = companionDef + classDef + "\n"
   }
 }
 
@@ -737,8 +737,9 @@ object Main {
       in("onKey", att("Boolean")),
     )
 
-    r += node("RNGStateLiteral")
     r += node("RNGSplit", in("state", child), in("dynBitstring", child))
+    r += node("RNGSplitStatic", in("state", child), in("staticUid", att("Long")))
+    r += node("RNGStateLiteral")
 
     val key = in("key", att("String").*)
 
@@ -1111,17 +1112,6 @@ object Main {
       errorID,
     ).withTraits(ApplyNode())
 
-    r += node(
-      "ApplySeeded",
-      in("function", att("String")),
-      in("_args", child.*),
-      in("rngState", child),
-      in("staticUID", att("Long")),
-      in("returnType", att("Type")),
-    ).withTraits(ApplyNode())
-      .withPreamble("val args = rngState +: _args")
-      .withPreamble("val typeArgs: Seq[Type] = Seq.empty[Type]")
-
     r += node(
       "ApplySpecial",
       in("function", att("String")),
@@ -1213,9 +1203,10 @@ object Main {
     val pack = "package is.hail.expr.ir.defs"
     val imports = Seq(
       "is.hail.annotations.Annotation",
+      "is.hail.collection.FastSeq",
       "is.hail.io.{AbstractTypedCodecSpec, BufferSpec}",
       "is.hail.types.virtual.{Type, TArray, TStream, TVoid, TStruct, TTuple}",
-      "is.hail.utils.{FastSeq, StringEscapeUtils}",
+      "is.hail.utils.StringEscapeUtils",
       "is.hail.expr.ir.{AggOp, BaseIR, IR, TableIR, MatrixIR, BlockMatrixIR, Name, UnaryOp, BinaryOp, " +
         "ComparisonOp, CanEmit, EmitParamType, TableWriter, " +
         "WrappedMatrixNativeMultiWriter, MatrixWriter, MatrixNativeMultiWriter, BlockMatrixWriter, " +
diff --git a/hail/hail/memory/package.mill b/hail/hail/memory/package.mill
new file mode 100644
index 00000000000..6e74496fb9b
--- /dev/null
+++ b/hail/hail/memory/package.mill
@@ -0,0 +1,16 @@
+package build.hail.memory
+
+import mill.{Cross, T}
+
+object `package` extends Cross[Memory]("debug", "release")
+trait Memory extends build.HailJavaModule, Cross.Module[String]:
+
+  override def moduleDir: os.Path =
+    super.moduleDir / crossValue
+
+  override def javacOptions: T[Seq[String]] =
+    super.javacOptions() ++ (
+      if scala.util.Properties.versionString.startsWith("1.8")
+        then Seq("-XDenableSunApiLintControl", "-Xlint:-sunapi")
+        else Seq()
+      )
\ No newline at end of file
diff --git a/hail/hail/package.mill b/hail/hail/package.mill
new file mode 100644
index 00000000000..2a60c3d4696
--- /dev/null
+++ b/hail/hail/package.mill
@@ -0,0 +1,197 @@
+package build.hail
+
+import mill.*
+import mill.api.{BuildCtx, Result}
+import mill.scalalib.*
+import mill.scalalib.Assembly.*
+import mill.scalalib.TestModule.TestNg
+import mill.util.{Jvm, VcsVersion}
+
+import build.Env
+import build.Settings
+import build.HailScalaModule
+
+import millbuild.BuildConfig.*
+import millbuild.BuildMode.*
+import millbuild.MvnCoordinate.*
+
+object `package` extends Cross[RootHailModule](enabledScalaVersions)
+
+trait RootHailModule extends CrossScalaModule, HailScalaModule:
+  outer =>
+
+  override def crossScalaVersion: String =
+    Settings.scalaMinorVersions(crossValue)
+
+  override def moduleDeps: Seq[JavaModule] =
+    Seq(
+      build.hail.utils(crossValue),
+      build.hail.memory(if buildMode == CI then "debug" else "release"),
+    )
+    
+  override def resources: T[Seq[PathRef]] =
+    super.resources() ++ Seq(
+      BuildCtx.withFilesystemCheckerDisabled {
+        PathRef(BuildCtx.workspaceRoot / "prebuilt" / "lib")
+      },
+    )
+
+  override def generatedSources: T[Seq[PathRef]] =
+    Task {
+      os.write(
+        Task.dest / "is" / "hail" / "package.scala",
+        f"""package is
+          |
+          |package object hail {
+          |  // FIXME: This should be a compiler switch/flag
+          |  val EmitTracebackInAssertions = ${buildMode != Release}
+          |  
+          |  val PipVersion = "${Settings.hailMajorMinorVersion}.${Settings.hailPatchVersion}"
+          |  val Revision = "${VcsVersion.vcsState().currentRevision}"
+          |  val SparkVersion = "${Env.sparkVersion()}"
+          |  
+          |  // FIXME: probably should use tags or something to choose English name
+          |  val PrettyVersion = PipVersion + "-" + Revision.substring(0, 12)
+          |}""".stripMargin,
+        createFolders = true,
+      )
+      
+      Seq(
+        PathRef(Task.dest),
+        build.hail.`ir-gen`.generate(),
+      )
+    }
+
+  override def unmanagedClasspath: T[Seq[PathRef]] =
+    Seq(build.hail.shadeazure.assembly())
+
+  // omit unmanagedClasspath from the jar
+  override def jar: T[PathRef] =
+    Task {
+      val jar = Task.dest / "out.jar"
+      Jvm.createJar(jar, (resources() ++ Seq(compile().classes)).map(_.path).filter(os.exists), manifest())
+      PathRef(jar)
+    }
+
+  override def bomMvnDeps: T[Seq[Dep]] =
+    Seq(
+      `asm-bom` :: "9.9",
+      `libraries-bom` :: "26.66.0",
+      `log4j-bom` :: "2.22.0",
+    )
+
+  override def compileMvnDeps: T[Seq[Dep]] =
+    Seq[Dep](
+      // WARNING WARNING WARNING
+      // Before changing the breeze version review:
+      // - https://hail.zulipchat.com/#narrow/stream/123011-Hail-Query-Dev/topic/new.20spark.20ndarray.20failures/near/41645
+      // - https://github.com/hail-is/hail/pull/11555
+      `breeze` :: "1.1",
+      `avro` :: "1.11.2",
+      `commons-codec` :: "1.16.1",
+      `commons-io` :: "2.16.1",
+      `commons-lang3` :: "3.12.0",
+      `commons-math3` :: "3.6.1",
+      `hadoop-client-api` :: "3.3.4",
+      `httpclient` :: "4.5.14",
+      `jackson-core` :: "2.15.2",
+      `json4s-jackson` :: "3.7.0-M11",
+      `lz4-java` :: "1.8.0",
+      `log4j-api`,
+      `log4j-core`,
+      `zstd-jni` :: "1.5.5-4",
+      `scalac-compat-annotation` :: "0.1.4",
+      (`spark-core` :: Env.sparkVersion()).excludeOrg("org.scalanlp"),
+      (`spark-mllib` :: Env.sparkVersion()).excludeOrg("org.scalanlp"),
+    )
+
+  override def mvnDeps: T[Seq[Dep]] =
+    Seq[Dep](
+      `all` :: "1.1.2",
+      `asm`,
+      `asm-analysis`,
+      `asm-util`,
+      `google-auth-library-oauth2-http`
+        .mvn
+        .excludeOrg(
+          "commons-codec",
+          "org.apache.httpcomponents",
+          "org.slf4j",
+        ),
+      `google-cloud-storage`
+        .mvn
+        .excludeOrg(
+          "com.fasterxml.jackson.core",
+          "commons-codec",
+          "org.slf4j",
+        ),
+      (`elasticsearch-spark` :: "9.2.1")
+        .excludeOrg(
+          "commons-logging",
+          "org.apache.spark",
+          "org.slf4j",
+        ),
+      `freemarker` :: "2.3.31",
+      (`htsjdk` :: "3.0.5").excludeOrg("*"),
+      (`jdistlib` :: "0.4.5").excludeOrg("*"),
+      `jna` :: "5.13.0",
+      (`log4j-api-scala` :: "13.1.0").excludeOrg("*"),
+      `scala-collection-compat`,
+      `sourcecode` :: "0.4.2",
+    )
+
+  override def runMvnDeps: T[Seq[Dep]] =
+    Seq(
+      (`breeze-natives` :: "1.1")
+        .excludeOrg(
+          "org.apache.commons",
+          "org.slf4j",
+        ),
+      `junixsocket-core` :: "2.6.1",
+    )
+
+  override def assemblyRules: Seq[Rule] =
+    super.assemblyRules ++ Seq(
+      Rule.Exclude("META-INF/INDEX.LIST"),
+      Rule.ExcludePattern("^scala/(?!collection/compat).*"),
+      Rule.AppendPattern("META-INF/services/.*", "\n"),
+      Rule.Relocate("breeze.**", "is.hail.relocated.@0"),
+      Rule.Relocate("com.google.**", "is.hail.relocated.@0"),
+      Rule.Relocate("scala.collection.compat.**", "is.hail.relocated.@0"),
+    )
+
+  override def scalacPluginMvnDeps: T[Seq[Dep]] =
+    super.scalacPluginMvnDeps() :+ (`better-monadic-for` :: "0.3.1")
+
+  def writeRunClasspath: T[PathRef] =
+    Task {
+      os.write(
+        Task.dest / "runClasspath",
+        runClasspath().map(_.path).mkString(":"),
+      )
+      PathRef(Task.dest)
+    }
+
+  object test extends HailScalaTests, TestNg, CrossValue:
+    override def forkArgs: T[Seq[String]] =
+      Seq("-Xss4m", "-Xmx4096M")
+
+    override def compileMvnDeps: T[Seq[Dep]] =
+      outer.compileMvnDeps()
+
+    override def mvnDeps: T[Seq[Dep]] =
+      outer.mvnDeps() ++ Seq(
+        `guice` :: "5.1.0",
+        `mockito-scala` :: "1.17.31",
+        `scalacheck` :: "1.18.1",
+        `scalacheck-1-18` :: "3.2.19.0",
+        `scalatest` :: "3.2.19",
+        `scalatest-shouldmatchers` :: "3.2.19",
+        `testng-7-10` :: "3.2.19.0",
+      )
+
+    override def runMvnDeps: T[Seq[Dep]] =
+      outer.runMvnDeps()
+
+    override def assemblyRules: Seq[Rule] =
+      outer.assemblyRules
diff --git a/hail/hail/shadeazure/package.mill b/hail/hail/shadeazure/package.mill
new file mode 100644
index 00000000000..6862b9b175a
--- /dev/null
+++ b/hail/hail/shadeazure/package.mill
@@ -0,0 +1,42 @@
+package build.hail.shadeazure
+
+import mill.T
+import mill.javalib.{Dep, JavaModule}
+import mill.javalib.Assembly.Rule
+
+import millbuild.MvnCoordinate.*
+
+object `package` extends JavaModule:
+
+  override def mvnDeps: T[Seq[Dep]] =
+    Seq(
+      `azure-core-http-netty` :: "1.13.7",
+      `azure-identity` :: "1.8.3",
+      `azure-storage-blob` :: "12.22.0",
+    )
+
+  override def assemblyRules: Seq[Rule] =
+    Seq(
+      Rule.ExcludePattern("META-INF/*.RSA"),
+      Rule.ExcludePattern("META-INF/*.SF"),
+      Rule.ExcludePattern("META-INF/*.DSA"),
+      Rule.Relocate("com.azure.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("com.ctc.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("com.fasterxml.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("com.microsoft.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("com.nimbusds.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("com.sun.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("io.netty.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("is.hail.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("net.jcip.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("net.minidev.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("org.apache.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("org.codehaus.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("org.objectweb.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("org.reactivestreams.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("org.slf4j.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("reactor.adapter.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("reactor.core.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("reactor.netty.**", "is.hail.shadedazure.@0"),
+      Rule.Relocate("reactor.util.**", "is.hail.shadedazure.@0"),
+    )
\ No newline at end of file
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/mutable/package.scala b/hail/hail/src-2.12/is/hail/utils/compat/mutable/package.scala
deleted file mode 100644
index 7c2ded2f508..00000000000
--- a/hail/hail/src-2.12/is/hail/utils/compat/mutable/package.scala
+++ /dev/null
@@ -1,6 +0,0 @@
-package is.hail.utils.compat
-
-package object mutable {
-  type Growable[-A] = scala.collection.generic.Growable[A]
-  type Shrinkable[-A] = scala.collection.generic.Shrinkable[A]
-}
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/package.scala b/hail/hail/src-2.12/is/hail/utils/compat/package.scala
deleted file mode 100644
index be947323f92..00000000000
--- a/hail/hail/src-2.12/is/hail/utils/compat/package.scala
+++ /dev/null
@@ -1,27 +0,0 @@
-package is.hail.utils
-
-import is.hail.utils.compat.immutable.ArraySeq
-
-import scala.collection.compat.Factory
-import scala.collection.mutable.WrappedArray
-import scala.reflect.ClassTag
-
-package compat {
-  class ArrayOps[A: ClassTag](val a: WrappedArray[A]) {
-    def sortInPlace[B >: A]()(implicit ct: ClassTag[B], ord: Ordering[B])
-      : WrappedArray[A] = {
-      scala.util.Sorting.stableSort(a.array.asInstanceOf[Array[B]])
-      a
-    }
-
-    def sortInPlaceBy[B](f: A => B)(implicit ord: Ordering[B]): WrappedArray[A] =
-      sortInPlace()(implicitly, ord = ord on f)
-  }
-}
-
-package object compat {
-  implicit def arraySeqbf[A: ClassTag](ob: ArraySeq.type): Factory[A, ArraySeq[A]] =
-    ob.canBuildFrom[A]
-
-  implicit def toArrayOps[A: ClassTag](a: Array[A]): ArrayOps[A] = new ArrayOps(a)
-}
diff --git a/hail/hail/src/is/hail/HailFeatureFlags.scala b/hail/hail/src/is/hail/HailFeatureFlags.scala
index b44360b7e48..326f8f0e59a 100644
--- a/hail/hail/src/is/hail/HailFeatureFlags.scala
+++ b/hail/hail/src/is/hail/HailFeatureFlags.scala
@@ -2,10 +2,10 @@ package is.hail
 
 import is.hail.backend.ExecutionCache
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{agg, Optimize}
 import is.hail.io.fs.RequesterPaysConfig
 import is.hail.types.encoded.EType
-import is.hail.utils._
 
 import scala.collection.mutable
 
@@ -73,13 +73,13 @@ class HailFeatureFlags private (
   }
 
   def +(feature: (String, String)): HailFeatureFlags =
-    new HailFeatureFlags(flags + (feature._1 -> feature._2))
+    new HailFeatureFlags(flags.clone() += feature._1 -> feature._2)
 
   def define(feature: String): HailFeatureFlags =
-    new HailFeatureFlags(flags + (feature -> "1"))
+    new HailFeatureFlags(flags.clone() += feature -> "1")
 
   def -(feature: String): HailFeatureFlags =
-    new HailFeatureFlags(flags - feature)
+    new HailFeatureFlags(flags.clone() -= feature)
 
   def get(flag: String): String = flags(flag)
 
diff --git a/hail/hail/src/is/hail/annotations/Annotation.scala b/hail/hail/src/is/hail/annotations/Annotation.scala
index 9f483f0c767..cf64879ae53 100644
--- a/hail/hail/src/is/hail/annotations/Annotation.scala
+++ b/hail/hail/src/is/hail/annotations/Annotation.scala
@@ -1,5 +1,6 @@
 package is.hail.annotations
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.types.virtual._
 import is.hail.utils._
 
diff --git a/hail/hail/src/is/hail/annotations/BroadcastValue.scala b/hail/hail/src/is/hail/annotations/BroadcastValue.scala
index ffd4cec0779..7761e5a6bd1 100644
--- a/hail/hail/src/is/hail/annotations/BroadcastValue.scala
+++ b/hail/hail/src/is/hail/annotations/BroadcastValue.scala
@@ -6,8 +6,9 @@ import is.hail.expr.ir.defs.EncodedLiteral
 import is.hail.io.{BufferSpec, Decoder, TypedCodecSpec}
 import is.hail.types.physical.{PArray, PStruct, PType}
 import is.hail.types.virtual.{TBaseStruct, TStruct}
-import is.hail.utils.{formatSpace, ArrayOfByteArrayOutputStream, Logging}
-import is.hail.utils.prettyPrint.ArrayOfByteArrayInputStream
+import is.hail.utils.{
+  formatSpace, ArrayOfByteArrayInputStream, ArrayOfByteArrayOutputStream, Logging,
+}
 
 import java.io.InputStream
 
@@ -99,9 +100,9 @@ trait BroadcastRegionValue extends Logging {
 case class BroadcastRow(ctx: ExecuteContext, value: RegionValue, t: PStruct)
     extends BroadcastRegionValue {
 
-  def javaValue: UnsafeRow = UnsafeRow.readBaseStruct(t, value.region, value.offset)
+  override def javaValue: UnsafeRow = UnsafeRow.readBaseStruct(t, value.region, value.offset)
 
-  def safeJavaValue: Row = SafeRow.read(t, value).asInstanceOf[Row]
+  override def safeJavaValue: Row = SafeRow.read(t, value).asInstanceOf[Row]
 
   def cast(newT: PStruct): BroadcastRow = {
     assert(t.virtualType == newT.virtualType)
@@ -128,9 +129,9 @@ case class BroadcastIndexedSeq(
   t: PArray,
 ) extends BroadcastRegionValue {
 
-  def safeJavaValue: IndexedSeq[Row] = SafeRow.read(t, value).asInstanceOf[IndexedSeq[Row]]
+  override def safeJavaValue: IndexedSeq[Row] = SafeRow.read(t, value).asInstanceOf[IndexedSeq[Row]]
 
-  def javaValue: UnsafeIndexedSeq = new UnsafeIndexedSeq(t, value.region, value.offset)
+  override def javaValue: UnsafeIndexedSeq = new UnsafeIndexedSeq(t, value.region, value.offset)
 
   def cast(newT: PArray): BroadcastIndexedSeq = {
     assert(t.virtualType == newT.virtualType)
diff --git a/hail/hail/src/is/hail/annotations/ChunkCache.scala b/hail/hail/src/is/hail/annotations/ChunkCache.scala
index 7ca5deb69cb..9cfc01a4d10 100644
--- a/hail/hail/src/is/hail/annotations/ChunkCache.scala
+++ b/hail/hail/src/is/hail/annotations/ChunkCache.scala
@@ -1,6 +1,6 @@
 package is.hail.annotations
 
-import is.hail.expr.ir.LongArrayBuilder
+import is.hail.collection.LongArrayBuilder
 
 import scala.collection.mutable
 
@@ -87,7 +87,7 @@ private class ChunkCache(allocator: Long => Long, freer: Long => Unit) {
       }
       // BiConsumer needed to work with scala 2.11.12
       bigChunkCache.forEach(new BiConsumer[Long, LongArrayBuilder]() {
-        def accept(key: Long, value: LongArrayBuilder): Unit =
+        override def accept(key: Long, value: LongArrayBuilder): Unit =
           while (value.size > 0) freeChunkFromMemory(pool, value.pop())
       })
     }
diff --git a/hail/hail/src/is/hail/annotations/ExtendedOrdering.scala b/hail/hail/src/is/hail/annotations/ExtendedOrdering.scala
index 87655121305..602876d0c9c 100644
--- a/hail/hail/src/is/hail/annotations/ExtendedOrdering.scala
+++ b/hail/hail/src/is/hail/annotations/ExtendedOrdering.scala
@@ -1,5 +1,6 @@
 package is.hail.annotations
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.utils._
 
 import org.apache.spark.sql.Row
@@ -9,7 +10,8 @@ object ExtendedOrdering {
     new ExtendedOrdering {
       val missingEqual = _missingEqual
 
-      def compareNonnull(x: T, y: T): Int = ord.compare(x.asInstanceOf[S], y.asInstanceOf[S])
+      override def compareNonnull(x: T, y: T): Int =
+        ord.compare(x.asInstanceOf[S], y.asInstanceOf[S])
 
       override def ltNonnull(x: T, y: T): Boolean = ord.lt(x.asInstanceOf[S], y.asInstanceOf[S])
 
@@ -24,7 +26,7 @@ object ExtendedOrdering {
     new ExtendedOrdering {
       val missingEqual = _missingEqual
 
-      def compareNonnull(x: T, y: T): Int = {
+      override def compareNonnull(x: T, y: T): Int = {
         val xit = x.asInstanceOf[Iterable[T]].iterator
         val yit = y.asInstanceOf[Iterable[T]].iterator
 
@@ -93,7 +95,7 @@ object ExtendedOrdering {
       // ord can be null if the element type is a TVariable
       val elemOrd = if (ord != null) ord.toOrdering else null
 
-      def compareNonnull(x: T, y: T): Int =
+      override def compareNonnull(x: T, y: T): Int =
         itOrd.compareNonnull(
           x.asInstanceOf[Array[T]].sorted(elemOrd).toFastSeq,
           y.asInstanceOf[Array[T]].sorted(elemOrd).toFastSeq,
@@ -124,7 +126,7 @@ object ExtendedOrdering {
 
       val missingEqual = _missingEqual
 
-      def compareNonnull(x: T, y: T): Int =
+      override def compareNonnull(x: T, y: T): Int =
         saOrd.compareNonnull(
           x.asInstanceOf[Iterable[T]].toArray,
           y.asInstanceOf[Iterable[T]].toArray,
@@ -158,7 +160,7 @@ object ExtendedOrdering {
       private def toArrayOfT(x: T): Array[T] =
         x.asInstanceOf[Map[_, _]].iterator.map { case (k, v) => Row(k, v): T }.toArray
 
-      def compareNonnull(x: T, y: T): Int =
+      override def compareNonnull(x: T, y: T): Int =
         saOrd.compareNonnull(
           toArrayOfT(x),
           toArrayOfT(y),
@@ -384,7 +386,7 @@ abstract class ExtendedOrdering extends Serializable {
 
     override def reverse: ExtendedOrdering = outer
 
-    def compareNonnull(x: T, y: T): Int = outer.compareNonnull(y, x)
+    override def compareNonnull(x: T, y: T): Int = outer.compareNonnull(y, x)
 
     override def ltNonnull(x: T, y: T): Boolean = outer.ltNonnull(y, x)
 
@@ -394,7 +396,7 @@ abstract class ExtendedOrdering extends Serializable {
   }
 
   def toOrdering: Ordering[T] = new Ordering[T] {
-    def compare(x: T, y: T): Int = outer.compare(x, y)
+    override def compare(x: T, y: T): Int = outer.compare(x, y)
 
     override def lt(x: T, y: T): Boolean = outer.lt(x, y)
 
diff --git a/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala b/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala
index a51d12cb8bc..e86ca5bfaf6 100644
--- a/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala
+++ b/hail/hail/src/is/hail/annotations/OrderedRVIterator.scala
@@ -1,10 +1,12 @@
 package is.hail.annotations
 
 import is.hail.backend.HailStateManager
+import is.hail.collection.{FlipbookIterator, StagingIterator, StateMachine}
+import is.hail.collection.compat.mutable.Growable
+import is.hail.collection.implicits.toRichIterator
 import is.hail.rvd.{RVDContext, RVDType}
 import is.hail.types.physical.PInterval
 import is.hail.utils._
-import is.hail.utils.compat.mutable.Growable
 
 import scala.collection.mutable
 
@@ -95,7 +97,7 @@ case class OrderedRVIterator(
         }
       }
 
-      def advance(): Unit = {
+      override def advance(): Unit = {
         left.advance()
         setValue()
       }
@@ -190,9 +192,9 @@ case class OrderedRVIterator(
       private val rvb = new RegionValueBuilder(sm, consumerRegion)
       private val rv = RegionValue()
 
-      def hasNext: Boolean = bit.hasNext || q.nonEmpty
+      override def hasNext: Boolean = bit.hasNext || q.nonEmpty
 
-      def next(): RegionValue = {
+      override def next(): RegionValue = {
         if (q.isEmpty) {
           do {
             val rv = bit.next()
diff --git a/hail/hail/src/is/hail/annotations/Region.scala b/hail/hail/src/is/hail/annotations/Region.scala
index 1031e019dbe..d8420ca70f3 100644
--- a/hail/hail/src/is/hail/annotations/Region.scala
+++ b/hail/hail/src/is/hail/annotations/Region.scala
@@ -417,7 +417,7 @@ final class Region protected[annotations] (
   def trackSharedChunk(addr: Long): Unit =
     memory.trackSharedChunk(addr)
 
-  def close(): Unit =
+  override def close(): Unit =
     invalidate()
 
   def addReferenceTo(r: Region): Unit =
diff --git a/hail/hail/src/is/hail/annotations/RegionMemory.scala b/hail/hail/src/is/hail/annotations/RegionMemory.scala
index 02e45222f4f..0b2becdd765 100644
--- a/hail/hail/src/is/hail/annotations/RegionMemory.scala
+++ b/hail/hail/src/is/hail/annotations/RegionMemory.scala
@@ -1,7 +1,7 @@
 package is.hail.annotations
 
-import is.hail.expr.ir.{AnyRefArrayBuilder, LongArrayBuilder}
-import is.hail.utils._
+import is.hail.collection.{AnyRefArrayBuilder, LongArrayBuilder}
+import is.hail.utils.implicits.toRichBoolean
 
 final class RegionMemory(pool: RegionPool) extends AutoCloseable {
   private[this] val usedBlocks = new LongArrayBuilder(4)
@@ -226,7 +226,7 @@ final class RegionMemory(pool: RegionPool) extends AutoCloseable {
     offsetWithinBlock = 0L
   }
 
-  def close(): Unit =
+  override def close(): Unit =
     free()
 
   def numChunks: Int = bigChunks.size
diff --git a/hail/hail/src/is/hail/annotations/RegionPool.scala b/hail/hail/src/is/hail/annotations/RegionPool.scala
index 492554be335..83489931ad1 100644
--- a/hail/hail/src/is/hail/annotations/RegionPool.scala
+++ b/hail/hail/src/is/hail/annotations/RegionPool.scala
@@ -1,6 +1,7 @@
 package is.hail.annotations
 
-import is.hail.expr.ir.LongArrayBuilder
+import is.hail.collection.LongArrayBuilder
+import is.hail.io.fs.readableBytes
 import is.hail.utils._
 
 import scala.collection.mutable
@@ -173,7 +174,7 @@ final class RegionPool private (strictMemoryCheck: Boolean, threadName: String,
 
   private[this] var closed: Boolean = false
 
-  def close(): Unit = {
+  override def close(): Unit = {
     if (closed)
       return
     closed = true
diff --git a/hail/hail/src/is/hail/annotations/RegionValueBuilder.scala b/hail/hail/src/is/hail/annotations/RegionValueBuilder.scala
index bc70f8d0683..1b34d0a3389 100644
--- a/hail/hail/src/is/hail/annotations/RegionValueBuilder.scala
+++ b/hail/hail/src/is/hail/annotations/RegionValueBuilder.scala
@@ -1,9 +1,11 @@
 package is.hail.annotations
 
 import is.hail.backend.HailStateManager
+import is.hail.collection.{IntArrayStack, LongArrayStack, ObjectArrayStack}
 import is.hail.types.physical._
 import is.hail.types.virtual._
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 
 class RegionValueBuilder(sm: HailStateManager, var region: Region) {
   def this(sm: HailStateManager) = this(sm, null)
diff --git a/hail/hail/src/is/hail/annotations/UnsafeOrdering.scala b/hail/hail/src/is/hail/annotations/UnsafeOrdering.scala
index 507531c8876..64de70999d6 100644
--- a/hail/hail/src/is/hail/annotations/UnsafeOrdering.scala
+++ b/hail/hail/src/is/hail/annotations/UnsafeOrdering.scala
@@ -1,8 +1,6 @@
 package is.hail.annotations
 
 abstract class UnsafeOrdering extends Ordering[Long] with Serializable {
-  def compare(o1: Long, o2: Long): Int
-
   def compare(rv1: RegionValue, rv2: RegionValue): Int =
     compare(rv1.offset, rv2.offset)
 
diff --git a/hail/hail/src/is/hail/annotations/UnsafeRow.scala b/hail/hail/src/is/hail/annotations/UnsafeRow.scala
index 6ef46397745..bcc7506fceb 100644
--- a/hail/hail/src/is/hail/annotations/UnsafeRow.scala
+++ b/hail/hail/src/is/hail/annotations/UnsafeRow.scala
@@ -13,10 +13,10 @@ import org.apache.spark.sql.Row
 import sun.reflect.generics.reflectiveObjects.NotImplementedException
 
 trait UnKryoSerializable extends KryoSerializable {
-  def write(kryo: Kryo, output: Output): Unit =
+  override def write(kryo: Kryo, output: Output): Unit =
     throw new NotImplementedException()
 
-  def read(kryo: Kryo, input: Input): Unit =
+  override def read(kryo: Kryo, input: Input): Unit =
     throw new NotImplementedException()
 }
 
@@ -28,7 +28,7 @@ class UnsafeIndexedSeq(
 
   val length: Int = t.loadLength(aoff)
 
-  def apply(i: Int): Annotation = {
+  override def apply(i: Int): Annotation = {
     if (i < 0 || i >= length)
       throw new IndexOutOfBoundsException(i.toString)
     if (t.isElementDefined(aoff, i)) {
@@ -156,19 +156,19 @@ class UnsafeRow(val t: PBaseStruct, var region: Region, var offset: Long)
 
   def set(rv: RegionValue): Unit = set(rv.region, rv.offset)
 
-  def length: Int = t.size
+  override def length: Int = t.size
 
   private def assertDefined(i: Int): Unit =
     if (isNullAt(i))
       throw new NullPointerException(s"null value at index $i")
 
-  def get(i: Int): Any =
+  override def get(i: Int): Any =
     if (isNullAt(i))
       null
     else
       UnsafeRow.read(t.types(i), region, t.loadField(offset, i))
 
-  def copy(): Row = new UnsafeRow(t, region, offset)
+  override def copy(): Row = new UnsafeRow(t, region, offset)
 
   def pretty(): String = Region.pretty(t, offset)
 
@@ -328,12 +328,12 @@ class UnsafeNDArray(val pnd: PNDArray, val region: Region, val ndAddr: Long) ext
   val elementType = pnd.elementType.virtualType
   val coordStorageArray = new Array[Long](shape.size)
 
-  def lookupElement(indices: IndexedSeq[Long]): Annotation = {
+  override def lookupElement(indices: IndexedSeq[Long]): Annotation = {
     val elementAddress = pnd.getElementAddress(indices, ndAddr)
     UnsafeRow.read(pnd.elementType, region, pnd.elementType.unstagedLoadFromNested(elementAddress))
   }
 
-  def getRowMajorElements(): IndexedSeq[Annotation] = {
+  override def getRowMajorElements(): IndexedSeq[Annotation] = {
     val indices = (0 until pnd.nDims).map(_ => 0L).toArray
     var curIdx = indices.size - 1
     var idxIntoFlat = 0
diff --git a/hail/hail/src/is/hail/annotations/ValueVisitor.scala b/hail/hail/src/is/hail/annotations/ValueVisitor.scala
index ff69277c889..25eedb54e62 100644
--- a/hail/hail/src/is/hail/annotations/ValueVisitor.scala
+++ b/hail/hail/src/is/hail/annotations/ValueVisitor.scala
@@ -45,50 +45,50 @@ final class PrettyVisitor extends ValueVisitor {
 
   @inline def result(): String = sb.result()
 
-  @inline def visitMissing(t: PType): Unit =
+  @inline override def visitMissing(t: PType): Unit =
     sb.append("NA")
 
-  @inline def visitBoolean(b: Boolean): Unit =
+  @inline override def visitBoolean(b: Boolean): Unit =
     sb.append(b)
 
-  @inline def visitInt32(i: Int): Unit =
+  @inline override def visitInt32(i: Int): Unit =
     sb.append(i)
 
-  @inline def visitInt64(l: Long): Unit =
+  @inline override def visitInt64(l: Long): Unit =
     sb.append(l)
 
-  @inline def visitFloat32(f: Float): Unit =
+  @inline override def visitFloat32(f: Float): Unit =
     sb.append(f)
 
-  @inline def visitFloat64(d: Double): Unit =
+  @inline override def visitFloat64(d: Double): Unit =
     sb.append(d)
 
-  @inline def visitBinary(a: Array[Byte]): Unit =
+  @inline override def visitBinary(a: Array[Byte]): Unit =
     sb.append("bytes...")
 
-  @inline def visitString(s: String): Unit =
+  @inline override def visitString(s: String): Unit =
     sb.append(s)
 
-  @inline def enterStruct(t: PStruct): Unit =
+  @inline override def enterStruct(t: PStruct): Unit =
     sb.append("{")
 
-  def enterField(f: PField): Unit = {
+  override def enterField(f: PField): Unit = {
     if (f.index > 0) sb += ','
     sb += ' ' ++= f.name ++= ": ": Unit
   }
 
-  @inline def leaveField(): Unit = {}
+  @inline override def leaveField(): Unit = {}
 
-  @inline def leaveStruct(): Unit =
+  @inline override def leaveStruct(): Unit =
     sb.append(" }")
 
-  @inline def enterTuple(t: PTuple): Unit =
+  @inline override def enterTuple(t: PTuple): Unit =
     sb.append('(')
 
-  @inline def leaveTuple(): Unit =
+  @inline override def leaveTuple(): Unit =
     sb.append(')')
 
-  def enterArray(t: PContainer, length: Int): Unit = {
+  override def enterArray(t: PContainer, length: Int): Unit = {
     t match {
       case _: PSet => sb.append("Set")
       case _: PDict => sb.append("Dict")
@@ -98,13 +98,13 @@ final class PrettyVisitor extends ValueVisitor {
     sb += '[' ++= length.toString += ';': Unit
   }
 
-  @inline def leaveArray(): Unit =
+  @inline override def leaveArray(): Unit =
     sb.append("]")
 
-  @inline def enterElement(i: Int): Unit = {
+  @inline override def enterElement(i: Int): Unit = {
     if (i > 0) sb += ','
     sb += ' '
   }
 
-  @inline def leaveElement(): Unit = {}
+  @inline override def leaveElement(): Unit = {}
 }
diff --git a/hail/hail/src/is/hail/annotations/WritableRegionValue.scala b/hail/hail/src/is/hail/annotations/WritableRegionValue.scala
index 4b864b94901..fda68a3c375 100644
--- a/hail/hail/src/is/hail/annotations/WritableRegionValue.scala
+++ b/hail/hail/src/is/hail/annotations/WritableRegionValue.scala
@@ -1,9 +1,9 @@
 package is.hail.annotations
 
 import is.hail.backend.HailStateManager
+import is.hail.collection.compat.mutable.GrowableCompat
 import is.hail.rvd.RVDContext
 import is.hail.types.physical.{PStruct, PType}
-import is.hail.utils.compat.mutable.GrowableCompat
 
 import scala.collection.mutable.{ArrayBuffer, PriorityQueue}
 
@@ -125,7 +125,7 @@ class RegionValuePriorityQueue(
     popped.region.close()
   }
 
-  def iterator: Iterator[RegionValue] = queue.iterator
+  override def iterator: Iterator[RegionValue] = queue.iterator
 }
 
 class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
@@ -140,7 +140,7 @@ class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
 
   override def knownSize: Int = idx.length
 
-  def addOne(rv: RegionValue): this.type =
+  override def addOne(rv: RegionValue): this.type =
     this.append(rv.region, rv.offset)
 
   def append(fromRegion: Region, fromOffset: Long): this.type = {
@@ -165,7 +165,7 @@ class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
     this
   }
 
-  def clear(): Unit = {
+  override def clear(): Unit = {
     region.clear()
     idx.clear()
     rvb.clear() // remove
@@ -174,16 +174,16 @@ class RegionValueArrayBuffer(val t: PType, region: Region, sm: HailStateManager)
   private var itIdx = 0
 
   private val it = new Iterator[RegionValue] {
-    def next(): RegionValue = {
+    override def next(): RegionValue = {
       value.setOffset(idx(itIdx))
       itIdx += 1
       value
     }
 
-    def hasNext: Boolean = itIdx < idx.size
+    override def hasNext: Boolean = itIdx < idx.size
   }
 
-  def iterator: Iterator[RegionValue] = {
+  override def iterator: Iterator[RegionValue] = {
     itIdx = 0
     it
   }
diff --git a/hail/hail/src/is/hail/asm4s/ClassBuilder.scala b/hail/hail/src/is/hail/asm4s/ClassBuilder.scala
index eee035ed9a4..032e3c4b623 100644
--- a/hail/hail/src/is/hail/asm4s/ClassBuilder.scala
+++ b/hail/hail/src/is/hail/asm4s/ClassBuilder.scala
@@ -1,8 +1,10 @@
 package is.hail.asm4s
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.lir
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.collection.mutable
 
@@ -209,7 +211,7 @@ class ModuleBuilder() {
 trait WrappedClassBuilder[C] extends WrappedModuleBuilder {
   def cb: ClassBuilder[C]
 
-  def modb: ModuleBuilder = cb.modb
+  override def modb: ModuleBuilder = cb.modb
 
   def className: String = cb.className
 
@@ -499,7 +501,7 @@ class ClassBuilder[C](
     new (HailClassLoader => C) with java.io.Serializable {
       @transient @volatile private var theClass: Class[_] = null
 
-      def apply(hcl: HailClassLoader): C = {
+      override def apply(hcl: HailClassLoader): C = {
         if (theClass == null) {
           this.synchronized {
             if (theClass == null) {
@@ -518,7 +520,7 @@ class ClassBuilder[C](
     new LocalRef[C](new lir.Parameter(null, 0, ti))
 
   val fieldBuilder: SettableBuilder = new SettableBuilder {
-    def newSettable[T](name: String)(implicit tti: TypeInfo[T]): Settable[T] =
+    override def newSettable[T](name: String)(implicit tti: TypeInfo[T]): Settable[T] =
       genFieldThisRef[T](name)
   }
 
@@ -625,7 +627,7 @@ object FunctionBuilder {
 trait WrappedMethodBuilder[C] extends WrappedClassBuilder[C] {
   def mb: MethodBuilder[C]
 
-  def cb: ClassBuilder[C] = mb.cb
+  override def cb: ClassBuilder[C] = mb.cb
 
   def methodName: String = mb.methodName
 
@@ -673,7 +675,8 @@ class MethodBuilder[C](
     cb.lclass.newMethod(methodName, parameterTypeInfo, returnTypeInfo, isStatic)
 
   val localBuilder: SettableBuilder = new SettableBuilder {
-    def newSettable[T](name: String)(implicit tti: TypeInfo[T]): Settable[T] = newLocal[T](name)
+    override def newSettable[T](name: String)(implicit tti: TypeInfo[T]): Settable[T] =
+      newLocal[T](name)
   }
 
   def this_ : Value[C] =
diff --git a/hail/hail/src/is/hail/asm4s/Code.scala b/hail/hail/src/is/hail/asm4s/Code.scala
index d9e7a71ba15..757e5568c4f 100644
--- a/hail/hail/src/is/hail/asm4s/Code.scala
+++ b/hail/hail/src/is/hail/asm4s/Code.scala
@@ -1,9 +1,10 @@
 package is.hail.asm4s
 
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.lir
 import is.hail.lir.{Block, ControlX, ValueX}
-import is.hail.utils._
 
 import scala.reflect.ClassTag
 
@@ -1082,7 +1083,7 @@ object Code {
   def _empty: Value[Unit] = Value.fromLIR[Unit](null: lir.ValueX)
 
   def _throwAny[T <: java.lang.Throwable]: Thrower[T] = new Thrower[T] {
-    def apply[U](cerr: Code[T])(implicit uti: TypeInfo[U]): Code[U] = {
+    override def apply[U](cerr: Code[T])(implicit uti: TypeInfo[U]): Code[U] = {
       if (uti eq UnitInfo) {
         cerr.end.append(lir.throwx(cerr.v))
         val newC = new VCode(cerr.start, cerr.end, null)
@@ -1214,7 +1215,7 @@ object Code {
       c.v match {
         case v: lir.LdcX =>
           val t = new Value[T] {
-            def get: Code[T] = Code(lir.ldcInsn(v.a, v.ti))
+            override def get: Code[T] = Code(lir.ldcInsn(v.a, v.ti))
           }
           return f(t)
         // You can't forward local references here because the local might have changed
@@ -1302,27 +1303,27 @@ class VCode[+T](
   // val stack = Thread.currentThread().getStackTrace
   // var clearStack: Array[StackTraceElement] = _
 
-  def start: lir.Block = {
+  override def start: lir.Block = {
     check()
     _start
   }
 
-  def end: lir.Block = {
+  override def end: lir.Block = {
     check()
     _end
   }
 
-  def v: lir.ValueX = {
+  override def v: lir.ValueX = {
     check()
     _v
   }
 
-  def check(): Unit =
+  override def check(): Unit =
     /* if (_start == null) { println(clearStack.mkString("\n")) println("-----")
      * println(stack.mkString("\n")) } */
     assert(_start != null)
 
-  def clear(): Unit = {
+  override def clear(): Unit = {
     /* if (clearStack != null) { println(clearStack.mkString("\n")) } assert(clearStack == null)
      * clearStack = Thread.currentThread().getStackTrace */
 
@@ -1364,17 +1365,17 @@ class CCode(
     _Lfalse
   }
 
-  def start: lir.Block = {
+  override def start: lir.Block = {
     checkV()
     _start
   }
 
-  def end: lir.Block = {
+  override def end: lir.Block = {
     checkV()
     _end
   }
 
-  def v: lir.ValueX = {
+  override def v: lir.ValueX = {
     checkV()
     _v
   }
@@ -1408,7 +1409,7 @@ class CCode(
     assert(_entry != null)
   }
 
-  def check(): Unit = {
+  override def check(): Unit = {
     if (_kind == null || _kind == CodeKind.C)
       assert(_entry != null)
     else {
@@ -1417,7 +1418,7 @@ class CCode(
     }
   }
 
-  def clear(): Unit = {
+  override def clear(): Unit = {
     _entry = null
     _Ltrue = null
     _Lfalse = null
@@ -1462,15 +1463,15 @@ class ConstCodeBoolean(val b: Boolean) extends Code[Boolean] {
 
   def toCCode: CCode = vc.toCCode
 
-  def start: lir.Block = vc.start
+  override def start: lir.Block = vc.start
 
-  def end: lir.Block = vc.end
+  override def end: lir.Block = vc.end
 
-  def v: lir.ValueX = vc.v
+  override def v: lir.ValueX = vc.v
 
-  def check(): Unit = vc.check()
+  override def check(): Unit = vc.check()
 
-  def clear(): Unit = vc.clear()
+  override def clear(): Unit = vc.clear()
 }
 
 class CodeBoolean(val lhs: Code[Boolean]) extends AnyVal {
@@ -1851,27 +1852,27 @@ class CodeLabel(val L: lir.Block) extends Code[Unit] {
 
   def isImplemented: Boolean = L.wellFormed
 
-  def start: lir.Block = {
+  override def start: lir.Block = {
     check()
     _start
   }
 
-  def end: lir.Block = {
+  override def end: lir.Block = {
     check()
     _start
   }
 
-  def v: lir.ValueX = {
+  override def v: lir.ValueX = {
     check()
     null
   }
 
-  def check(): Unit =
+  override def check(): Unit =
     /* if (_start == null) { println(clearStack.mkString("\n")) println("-----")
      * println(stack.mkString("\n")) } */
     assert(_start != null)
 
-  def clear(): Unit =
+  override def clear(): Unit =
     /* if (clearStack != null) { println(clearStack.mkString("\n")) } assert(clearStack == null)
      * clearStack = Thread.currentThread().getStackTrace */
     _start = null
@@ -2004,7 +2005,7 @@ object FieldRef {
 
 object Value {
   def fromLIR[T](v: => lir.ValueX): Value[T] = new Value[T] {
-    def get: Code[T] = Code(v)
+    override def get: Code[T] = Code(v)
   }
 }
 
@@ -2040,23 +2041,23 @@ class ThisLazyFieldRef[T: TypeInfo](cb: ClassBuilder[_], name: String, setup: Co
 class ThisFieldRef[T: TypeInfo](cb: ClassBuilder[_], f: Field[T]) extends Settable[T] {
   def name: String = f.name
 
-  def get: Code[T] = f.get(cb.this_)
+  override def get: Code[T] = f.get(cb.this_)
 
-  def store(rhs: Code[T]): Code[Unit] = f.put(cb.this_, rhs)
+  override def store(rhs: Code[T]): Code[Unit] = f.put(cb.this_, rhs)
 }
 
 class StaticFieldRef[T: TypeInfo](f: StaticField[T]) extends Settable[T] {
   def name: String = f.name
 
-  def get: Code[T] = f.get()
+  override def get: Code[T] = f.get()
 
-  def store(rhs: Code[T]): Code[Unit] = f.put(rhs)
+  override def store(rhs: Code[T]): Code[Unit] = f.put(rhs)
 }
 
 class LocalRef[T](val l: lir.Local) extends Settable[T] {
-  def get: Code[T] = Code(lir.load(l))
+  override def get: Code[T] = Code(lir.load(l))
 
-  def store(rhs: Code[T]): Code[Unit] = {
+  override def store(rhs: Code[T]): Code[Unit] = {
     assert(rhs.v != null)
     rhs.end.append(lir.store(l, rhs.v))
     val newC = new VCode(rhs.start, rhs.end, null)
@@ -2090,7 +2091,7 @@ class FieldRef[T, S](f: reflect.Field)(implicit tct: ClassTag[T], sti: TypeInfo[
 
   def getField(lhs: Value[T]): Value[S] =
     new Value[S] {
-      def get: Code[S] = self.getField(if (lhs != null) lhs.get else null)
+      override def get: Code[S] = self.getField(if (lhs != null) lhs.get else null)
     }
 
   def getField(lhs: Code[T]): Code[S] =
diff --git a/hail/hail/src/is/hail/asm4s/CodeBuilder.scala b/hail/hail/src/is/hail/asm4s/CodeBuilder.scala
index 16470cb68ca..f8e150da7a1 100644
--- a/hail/hail/src/is/hail/asm4s/CodeBuilder.scala
+++ b/hail/hail/src/is/hail/asm4s/CodeBuilder.scala
@@ -1,7 +1,8 @@
 package is.hail.asm4s
 
-import is.hail.{lir, HAIL_BUILD_CONFIGURATION}
-import is.hail.utils.{toRichIterable, Traceback}
+import is.hail.{lir, EmitTracebackInAssertions}
+import is.hail.collection.implicits.toRichIterable
+import is.hail.utils.Traceback
 
 import scala.collection.compat._
 
@@ -274,18 +275,19 @@ trait CodeBuilderLike {
 
   def _assert(cond: => Code[Boolean], msgs: Code[String]*): Unit = {
     val message = msgs.reduce(_.concat(_))
-    if (HAIL_BUILD_CONFIGURATION.isDebug) {
-      val traceback = mb.cb.modb.getObject[Throwable](new Traceback().fillInStackTrace())
-      val assertion = Code.newInstance[AssertionError, String, Throwable](message, traceback)
-      if_(cond, {}, _throw(assertion))
-    } else {
-      if_(cond, {}, _throw(Code.newInstance[AssertionError, Object](message)))
-    }
+
+    val assertion =
+      if (EmitTracebackInAssertions) {
+        val traceback = mb.cb.modb.getObject[Throwable](new Traceback().fillInStackTrace())
+        Code.newInstance[AssertionError, String, Throwable](message, traceback)
+      } else Code.newInstance[AssertionError, Object](message)
+
+    if_(cond, {}, _throw(assertion))
   }
 }
 
 class CodeBuilder(val mb: MethodBuilder[_], var code: Code[Unit]) extends CodeBuilderLike {
-  def isOpenEnded: Boolean =
+  override def isOpenEnded: Boolean =
     code.isOpenEnded
 
   override def append(c: Code[Unit]): Unit = {
@@ -305,7 +307,7 @@ class CodeBuilder(val mb: MethodBuilder[_], var code: Code[Unit]) extends CodeBu
   def uncheckedAppend(c: Code[Unit]): Unit =
     code = Code(code, c)
 
-  def result(): Code[Unit] = {
+  override def result(): Code[Unit] = {
     val tmp = code
     code = Code._empty
     tmp
diff --git a/hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala b/hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala
index 372cdaaf82a..c6d35efeb09 100644
--- a/hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala
+++ b/hail/hail/src/is/hail/asm4s/GenericTypeInfo.scala
@@ -16,7 +16,7 @@ object GenericTypeInfo {
 final class GenericTypeInfo[T: TypeInfo]() extends MaybeGenericTypeInfo[T] {
   val base = typeInfo[T]
 
-  def castFromGeneric(cb: CodeBuilderLike, _x: Value[_]): Value[T] = {
+  override def castFromGeneric(cb: CodeBuilderLike, _x: Value[_]): Value[T] = {
     val x = coerce[AnyRef](_x)
     base match {
       case _: IntInfo.type =>
@@ -44,7 +44,7 @@ final class GenericTypeInfo[T: TypeInfo]() extends MaybeGenericTypeInfo[T] {
     }
   }
 
-  def castToGeneric(cb: CodeBuilderLike, x: Value[T]): Value[_] = base match {
+  override def castToGeneric(cb: CodeBuilderLike, x: Value[T]): Value[_] = base match {
     case _: IntInfo.type =>
       cb.memoize(Code.boxInt(coerce[Int](x)))
     case _: LongInfo.type =>
@@ -78,8 +78,8 @@ object NotGenericTypeInfo {
 }
 
 final class NotGenericTypeInfo[T: TypeInfo]() extends MaybeGenericTypeInfo[T] {
-  def castFromGeneric(cb: CodeBuilderLike, x: Value[_]): Value[T] = coerce[T](x)
-  def castToGeneric(cb: CodeBuilderLike, x: Value[T]): Value[_] = x
+  override def castFromGeneric(cb: CodeBuilderLike, x: Value[_]): Value[T] = coerce[T](x)
+  override def castToGeneric(cb: CodeBuilderLike, x: Value[T]): Value[_] = x
 
   val base = typeInfo[T]
   val generic = base
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichCodeInputBuffer.scala b/hail/hail/src/is/hail/asm4s/implicits/RichCodeInputBuffer.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/richUtils/RichCodeInputBuffer.scala
rename to hail/hail/src/is/hail/asm4s/implicits/RichCodeInputBuffer.scala
index 1fec9f5f73c..63d939c4a37 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichCodeInputBuffer.scala
+++ b/hail/hail/src/is/hail/asm4s/implicits/RichCodeInputBuffer.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.asm4s.implicits
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, _}
@@ -7,7 +7,6 @@ import is.hail.io.InputBuffer
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual._
-import is.hail.utils._
 
 class RichCodeInputBuffer(
   val ib: Value[InputBuffer]
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichCodeIterator.scala b/hail/hail/src/is/hail/asm4s/implicits/RichCodeIterator.scala
similarity index 89%
rename from hail/hail/src/is/hail/utils/richUtils/RichCodeIterator.scala
rename to hail/hail/src/is/hail/asm4s/implicits/RichCodeIterator.scala
index d091eeab5eb..1e6cca93f0e 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichCodeIterator.scala
+++ b/hail/hail/src/is/hail/asm4s/implicits/RichCodeIterator.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.asm4s.implicits
 
 import is.hail.asm4s.{Code, TypeInfo}
 
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichCodeOutputBuffer.scala b/hail/hail/src/is/hail/asm4s/implicits/RichCodeOutputBuffer.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/richUtils/RichCodeOutputBuffer.scala
rename to hail/hail/src/is/hail/asm4s/implicits/RichCodeOutputBuffer.scala
index 539da999918..c423d95d399 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichCodeOutputBuffer.scala
+++ b/hail/hail/src/is/hail/asm4s/implicits/RichCodeOutputBuffer.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.asm4s.implicits
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichCodeRegion.scala b/hail/hail/src/is/hail/asm4s/implicits/RichCodeRegion.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/richUtils/RichCodeRegion.scala
rename to hail/hail/src/is/hail/asm4s/implicits/RichCodeRegion.scala
index 1a203f62611..8568ae2278b 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichCodeRegion.scala
+++ b/hail/hail/src/is/hail/asm4s/implicits/RichCodeRegion.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.asm4s.implicits
 
 import is.hail.annotations.{Region, RegionMemory, RegionPool}
 import is.hail.asm4s._
diff --git a/hail/hail/src/is/hail/asm4s/implicits/package.scala b/hail/hail/src/is/hail/asm4s/implicits/package.scala
new file mode 100644
index 00000000000..298d836ba53
--- /dev/null
+++ b/hail/hail/src/is/hail/asm4s/implicits/package.scala
@@ -0,0 +1,24 @@
+package is.hail.asm4s
+
+import is.hail.annotations.Region
+import is.hail.io.{InputBuffer, OutputBuffer}
+
+package object implicits {
+  implicit def valueToRichCodeInputBuffer(in: Value[InputBuffer]): RichCodeInputBuffer =
+    new RichCodeInputBuffer(in)
+
+  implicit def valueToRichCodeOutputBuffer(out: Value[OutputBuffer]): RichCodeOutputBuffer =
+    new RichCodeOutputBuffer(out)
+
+  implicit def toRichCodeIterator[T](it: Code[Iterator[T]]): RichCodeIterator[T] =
+    new RichCodeIterator[T](it)
+
+  implicit def valueToRichCodeIterator[T](it: Value[Iterator[T]]): RichCodeIterator[T] =
+    new RichCodeIterator[T](it)
+
+  implicit def codeToRichCodeRegion(region: Code[Region]): RichCodeRegion =
+    new RichCodeRegion(region)
+
+  implicit def valueToRichCodeRegion(region: Value[Region]): RichCodeRegion =
+    new RichCodeRegion(region)
+}
diff --git a/hail/hail/src/is/hail/asm4s/package.scala b/hail/hail/src/is/hail/asm4s/package.scala
index b3d24da6e10..49ce98e7f0d 100644
--- a/hail/hail/src/is/hail/asm4s/package.scala
+++ b/hail/hail/src/is/hail/asm4s/package.scala
@@ -51,7 +51,7 @@ package asm4s {
     val astoreOp = AASTORE
     val returnOp = ARETURN
 
-    def newArray(): AbstractInsnNode = new TypeInsnNode(ANEWARRAY, iname)
+    override def newArray(): AbstractInsnNode = new TypeInsnNode(ANEWARRAY, iname)
 
     override def uninitializedValue: Value[_] = Code._uncheckednull(this)
   }
@@ -65,7 +65,7 @@ package asm4s {
     val astoreOp = AASTORE
     val returnOp = ARETURN
 
-    def newArray() = new TypeInsnNode(ANEWARRAY, iname)
+    override def newArray() = new TypeInsnNode(ANEWARRAY, iname)
 
     override def uninitializedValue: Value[_] = Code._null[Array[T]](this)
   }
@@ -130,7 +130,7 @@ package object asm4s {
     val returnOp = IRETURN
     val newarrayOp = NEWARRAY
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_BOOLEAN)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_BOOLEAN)
 
     override def uninitializedValue: Value[_] = const(false)
   }
@@ -144,7 +144,7 @@ package object asm4s {
     val returnOp = IRETURN
     val newarrayOp = NEWARRAY
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_BYTE)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_BYTE)
 
     override def uninitializedValue: Value[_] = const(0.toByte)
   }
@@ -158,7 +158,7 @@ package object asm4s {
     val returnOp = IRETURN
     val newarrayOp = NEWARRAY
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_SHORT)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_SHORT)
 
     override def uninitializedValue: Value[_] = const(0.toShort)
   }
@@ -171,7 +171,7 @@ package object asm4s {
     val astoreOp = IASTORE
     val returnOp = IRETURN
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_INT)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_INT)
 
     override def uninitializedValue: Value[_] = const(0)
   }
@@ -185,7 +185,7 @@ package object asm4s {
     val returnOp = LRETURN
     override val slots = 2
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_LONG)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_LONG)
 
     override def uninitializedValue: Value[_] = const(0L)
   }
@@ -198,7 +198,7 @@ package object asm4s {
     val astoreOp = FASTORE
     val returnOp = FRETURN
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_FLOAT)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_FLOAT)
 
     override def uninitializedValue: Value[_] = const(0f)
   }
@@ -212,7 +212,7 @@ package object asm4s {
     val returnOp = DRETURN
     override val slots = 2
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_DOUBLE)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_DOUBLE)
 
     override def uninitializedValue: Value[_] = const(0d)
   }
@@ -226,21 +226,21 @@ package object asm4s {
     val returnOp = IRETURN
     override val slots = 2
 
-    def newArray() = new IntInsnNode(NEWARRAY, T_CHAR)
+    override def newArray() = new IntInsnNode(NEWARRAY, T_CHAR)
 
     override def uninitializedValue: Value[_] = const(0.toChar)
   }
 
   implicit object UnitInfo extends TypeInfo[Unit] {
     val desc = "V"
-    def loadOp = ???
-    def storeOp = ???
-    def aloadOp = ???
-    def astoreOp = ???
+    override def loadOp = ???
+    override def storeOp = ???
+    override def aloadOp = ???
+    override def astoreOp = ???
     val returnOp = RETURN
     override def slots = ???
 
-    def newArray() = ???
+    override def newArray() = ???
 
     override def uninitializedValue: Value[_] = Code._empty
   }
@@ -354,7 +354,7 @@ package object asm4s {
   }
 
   implicit def const(b: Boolean): Value[Boolean] = new Value[Boolean] {
-    def get: Code[Boolean] = new ConstCodeBoolean(b)
+    override def get: Code[Boolean] = new ConstCodeBoolean(b)
   }
 
   implicit def const(i: Int): Value[Int] = _const(i, IntInfo)
diff --git a/hail/hail/src/is/hail/backend/BackendUtils.scala b/hail/hail/src/is/hail/backend/BackendUtils.scala
index dd6af720daf..3600c425f00 100644
--- a/hail/hail/src/is/hail/backend/BackendUtils.scala
+++ b/hail/hail/src/is/hail/backend/BackendUtils.scala
@@ -2,6 +2,7 @@ package is.hail.backend
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.implicits.toRichIndexedSeq
 import is.hail.expr.ir.analyses.SemanticHash
 import is.hail.expr.ir.lowering.TableStageDependency
 import is.hail.io.fs._
diff --git a/hail/hail/src/is/hail/backend/ExecuteContext.scala b/hail/hail/src/is/hail/backend/ExecuteContext.scala
index e03577c61d6..8e5b1b4856d 100644
--- a/hail/hail/src/is/hail/backend/ExecuteContext.scala
+++ b/hail/hail/src/is/hail/backend/ExecuteContext.scala
@@ -161,7 +161,7 @@ class ExecuteContext(
 
   def shouldLogIR(): Boolean = !shouldNotLogIR()
 
-  def close(): Unit = {
+  override def close(): Unit = {
     tempFileManager.close()
     taskContext.close()
   }
diff --git a/hail/hail/src/is/hail/backend/ExecutionCache.scala b/hail/hail/src/is/hail/backend/ExecutionCache.scala
index 62fcd1960a9..2cea980a049 100644
--- a/hail/hail/src/is/hail/backend/ExecutionCache.scala
+++ b/hail/hail/src/is/hail/backend/ExecutionCache.scala
@@ -27,7 +27,7 @@ case object ExecutionCache {
     if (Option(flags.get(Flags.UseFastRestarts)).isEmpty) noCache
     else fsCache(
       fs,
-      Option(flags.get(Flags.Cachedir)).getOrElse(s"$tmpdir/hail/${is.hail.HAIL_PIP_VERSION}"),
+      Option(flags.get(Flags.Cachedir)).getOrElse(s"$tmpdir/hail/${is.hail.PipVersion}"),
     )
 
   def fsCache(fs: FS, cachedir: String): ExecutionCache = {
diff --git a/hail/hail/src/is/hail/backend/HailTaskContext.scala b/hail/hail/src/is/hail/backend/HailTaskContext.scala
index 41f82c7cba4..01d662044d1 100644
--- a/hail/hail/src/is/hail/backend/HailTaskContext.scala
+++ b/hail/hail/src/is/hail/backend/HailTaskContext.scala
@@ -30,12 +30,6 @@ abstract class HailTaskContext extends AutoCloseable with Logging {
 
   def getRegionPool(): RegionPool = thePool
 
-  def partSuffix(): String = {
-    val rng = new java.security.SecureRandom()
-    val fileUUID = new java.util.UUID(rng.nextLong(), rng.nextLong())
-    s"${stageId()}-${partitionId()}-${attemptNumber()}-$fileUUID"
-  }
-
   val finalizers = mutable.ArrayBuffer.empty[TaskFinalizer]
 
   def newFinalizer(): TaskFinalizer = {
@@ -44,7 +38,7 @@ abstract class HailTaskContext extends AutoCloseable with Logging {
     f
   }
 
-  def close(): Unit = {
+  override def close(): Unit = {
     logger.info(
       s"TaskReport: stage=${stageId()}, partition=${partitionId()}, attempt=${attemptNumber()}, " +
         s"peakBytes=${thePool.getHighestTotalUsage}, peakBytesReadable=${formatSpace(thePool.getHighestTotalUsage)}, " +
diff --git a/hail/hail/src/is/hail/backend/driver/BackendRpc.scala b/hail/hail/src/is/hail/backend/driver/BackendRpc.scala
index 21f45f371af..b0187953905 100644
--- a/hail/hail/src/is/hail/backend/driver/BackendRpc.scala
+++ b/hail/hail/src/is/hail/backend/driver/BackendRpc.scala
@@ -1,6 +1,7 @@
 package is.hail.backend.driver
 
 import is.hail.backend.{Backend, ExecuteContext}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.IRParser
 import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.expr.ir.functions.IRFunctionRegistry.UserDefinedFnKey
@@ -9,7 +10,7 @@ import is.hail.io.plink.LoadPlink
 import is.hail.io.vcf.LoadVCF
 import is.hail.types.virtual.{Kind, TFloat64}
 import is.hail.types.virtual.Kinds._
-import is.hail.utils.{jsonToBytes, using, ExecutionTimer, FastSeq}
+import is.hail.utils.{jsonToBytes, using, ExecutionTimer}
 import is.hail.utils.ExecutionTimer.Timings
 import is.hail.variant.ReferenceGenome
 
diff --git a/hail/hail/src/is/hail/backend/driver/BatchQueryDriver.scala b/hail/hail/src/is/hail/backend/driver/BatchQueryDriver.scala
index eb4d49b7d48..dceca491b1f 100644
--- a/hail/hail/src/is/hail/backend/driver/BatchQueryDriver.scala
+++ b/hail/hail/src/is/hail/backend/driver/BatchQueryDriver.scala
@@ -1,10 +1,12 @@
 package is.hail.backend.driver
 
-import is.hail.{HAIL_PRETTY_VERSION, HailFeatureFlags}
+import is.hail.{HailFeatureFlags, PrettyVersion}
 import is.hail.annotations.Memory
 import is.hail.asm4s.HailClassLoader
 import is.hail.backend.{Backend, ExecuteContext, OwningTempFileManager}
 import is.hail.backend.service._
+import is.hail.collection.ImmutableMap
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.lowering.IrMetadata
 import is.hail.io.fs.{CloudStorageFSConfig, FS, RouterFS}
 import is.hail.io.reference.{IndexedFastaSequenceFile, LiftOver}
@@ -134,7 +136,7 @@ object BatchQueryDriver extends HttpLikeRpc with Logging {
     val inputURL = argv(5)
     val outputURL = argv(6)
 
-    logger.info(f"${getClass.getName} $HAIL_PRETTY_VERSION")
+    logger.info(f"${getClass.getName} $PrettyVersion")
 
     sys.env.get("HAIL_SSL_CONFIG_DIR").foreach(tls.setSSLConfigFromDir)
 
@@ -239,7 +241,7 @@ private class HailSocketAPIOutputStream(
 
   def writeString(s: String): Unit = writeBytes(s.getBytes(StandardCharsets.UTF_8))
 
-  def close(): Unit =
+  override def close(): Unit =
     if (!closed) {
       out.close()
       closed = true
diff --git a/hail/hail/src/is/hail/backend/driver/Py4JQueryDriver.scala b/hail/hail/src/is/hail/backend/driver/Py4JQueryDriver.scala
index 2d85760e4f2..29aa21075f9 100644
--- a/hail/hail/src/is/hail/backend/driver/Py4JQueryDriver.scala
+++ b/hail/hail/src/is/hail/backend/driver/Py4JQueryDriver.scala
@@ -4,6 +4,8 @@ import is.hail.{linalg, HailFeatureFlags}
 import is.hail.asm4s.HailClassLoader
 import is.hail.backend._
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.{JSONAnnotationImpex, SparkAnnotationImpex}
 import is.hail.expr.ir._
 import is.hail.expr.ir.IRParser.parseType
@@ -13,14 +15,17 @@ import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.expr.ir.lowering.IrMetadata
 import is.hail.io.fs._
 import is.hail.io.reference.{IndexedFastaSequenceFile, LiftOver}
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical.PStruct
 import is.hail.types.virtual.{TArray, TInterval}
 import is.hail.types.virtual.Kinds.{BlockMatrix, Matrix, Table, Value}
 import is.hail.utils._
 import is.hail.utils.ExecutionTimer.Timings
+import is.hail.utils.implicits.toRichString
 import is.hail.variant.ReferenceGenome
 
 import scala.annotation.nowarn
+import scala.collection.compat._
 import scala.collection.mutable
 import scala.jdk.CollectionConverters._
 
@@ -302,7 +307,7 @@ final class Py4JQueryDriver(backend: Backend) extends Closeable with Logging {
 
   def pyGrepReturn(regex: String, files: Seq[String], maxLines: Int)
     : Array[(String, Array[String])] =
-    fileAndLineCounts(regex, files, maxLines).mapValues(_.map(_.value)).toArray
+    fileAndLineCounts(regex, files, maxLines).view.mapValues(_.map(_.value)).toArray
 
   private[this] def addReference(rg: ReferenceGenome): Unit =
     ReferenceGenome.addFatalOnCollision(references, FastSeq(rg))
@@ -473,7 +478,7 @@ final class Py4JQueryDriver(backend: Backend) extends Closeable with Logging {
       // Note that simply calling httpServer.start() from a non-daemon thread will spawn a
       // non-daemon thread itself.
       private[this] val thread = new Thread(new Runnable() {
-        def run(): Unit = httpServer.start()
+        override def run(): Unit = httpServer.start()
       })
 
       thread.setDaemon(true)
diff --git a/hail/hail/src/is/hail/backend/local/LocalBackend.scala b/hail/hail/src/is/hail/backend/local/LocalBackend.scala
index a869f30b483..c04bdc66afb 100644
--- a/hail/hail/src/is/hail/backend/local/LocalBackend.scala
+++ b/hail/hail/src/is/hail/backend/local/LocalBackend.scala
@@ -2,6 +2,7 @@ package is.hail.backend.local
 
 import is.hail.backend._
 import is.hail.backend.Backend.PartitionFn
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Validate
 import is.hail.expr.ir._
 import is.hail.expr.ir.analyses.SemanticHash
@@ -9,7 +10,6 @@ import is.hail.expr.ir.lowering._
 import is.hail.types._
 import is.hail.types.physical.PTuple
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.reflect.ClassTag
 import scala.util.control.NonFatal
@@ -40,7 +40,7 @@ object LocalBackend extends Backend with Logging {
 
   is.hail.linalg.registerImplOpMulMatrix_DMD_DVD_eq_DVD
 
-  def broadcast[T: ClassTag](value: T): BroadcastValue[T] =
+  override def broadcast[T: ClassTag](value: T): BroadcastValue[T] =
     new LocalBroadcastValue[T](value)
 
   private[this] var stageIdx: Int = 0
@@ -100,9 +100,9 @@ object LocalBackend extends Backend with Logging {
     }
   }
 
-  def defaultParallelism: Int = 1
+  override def defaultParallelism: Int = 1
 
-  def close(): Unit =
+  override def close(): Unit =
     synchronized { stageIdx = 0 }
 
   private[this] def _jvmLowerAndExecute(
@@ -140,7 +140,7 @@ object LocalBackend extends Backend with Logging {
   ): TableReader =
     LowerDistributedSort.distributedSort(ctx, stage, sortFields, rt, nPartitions)
 
-  def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
+  override def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
     : TableStage =
     LowerTableIR.applyTable(inputIR, DArrayLowering.All, ctx, analyses)
 }
diff --git a/hail/hail/src/is/hail/backend/service/ServiceBackend.scala b/hail/hail/src/is/hail/backend/service/ServiceBackend.scala
index 9d2820a18ac..a82f389af8e 100644
--- a/hail/hail/src/is/hail/backend/service/ServiceBackend.scala
+++ b/hail/hail/src/is/hail/backend/service/ServiceBackend.scala
@@ -1,10 +1,12 @@
 package is.hail.backend.service
 
-import is.hail.HAIL_REVISION
+import is.hail.Revision
 import is.hail.backend._
 import is.hail.backend.Backend.PartitionFn
 import is.hail.backend.local.LocalTaskContext
 import is.hail.backend.service.ServiceBackend.MaxAvailableGcsConnections
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Validate
 import is.hail.expr.ir.{
   CompileAndEvaluate, IR, IRSize, LoweringAnalyses, SortField, TableIR, TableReader, TypeCheck,
@@ -17,7 +19,6 @@ import is.hail.services.oauth2.{CloudCredentials, HailCredentials}
 import is.hail.types._
 import is.hail.types.physical._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 import scala.concurrent.{Await, CancellationException, ExecutionContext, Future}
@@ -82,7 +83,7 @@ object ServiceBackend {
     new ServiceBackend(
       name,
       client,
-      GitRevision(HAIL_REVISION),
+      GitRevision(Revision),
       BatchConfig(batchId, 0),
       workerConfig,
     )
@@ -112,11 +113,11 @@ class ServiceBackend(
       Executors.newFixedThreadPool(MaxAvailableGcsConnections)
     }
 
-  def defaultParallelism: Int = 4
+  override def defaultParallelism: Int = 4
 
-  def broadcast[T: ClassTag](_value: T): BroadcastValue[T] =
+  override def broadcast[T: ClassTag](_value: T): BroadcastValue[T] =
     new BroadcastValue[T] with Serializable {
-      def value: T = _value
+      override def value: T = _value
     }
 
   override def runtimeContext(ctx: ExecuteContext): DriverRuntimeContext =
@@ -409,7 +410,7 @@ class ServiceBackend(
   ): TableReader =
     LowerDistributedSort.distributedSort(ctx, inputStage, sortFields, rt, nPartitions)
 
-  def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
+  override def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
     : TableStage =
     LowerTableIR.applyTable(inputIR, DArrayLowering.All, ctx, analyses)
 }
diff --git a/hail/hail/src/is/hail/backend/service/Worker.scala b/hail/hail/src/is/hail/backend/service/Worker.scala
index d00de18b6de..cfb9c55babf 100644
--- a/hail/hail/src/is/hail/backend/service/Worker.scala
+++ b/hail/hail/src/is/hail/backend/service/Worker.scala
@@ -1,6 +1,6 @@
 package is.hail.backend.service
 
-import is.hail.{HAIL_REVISION, HailFeatureFlags}
+import is.hail.{HailFeatureFlags, Revision}
 import is.hail.asm4s._
 import is.hail.backend.Backend.PartitionFn
 import is.hail.backend.HailTaskContext
@@ -176,7 +176,7 @@ object Worker extends Logging {
 
     sys.env.get("HAIL_SSL_CONFIG_DIR").foreach(tls.setSSLConfigFromDir)
 
-    logger.info(s"${getClass.getName} $HAIL_REVISION")
+    logger.info(s"${getClass.getName} $Revision")
     logger.info(s"running partition $partition root '$root' with scratch directory '$scratchDir'")
 
     timer.start(s"partition $partition")
diff --git a/hail/hail/src/is/hail/backend/spark/SparkBackend.scala b/hail/hail/src/is/hail/backend/spark/SparkBackend.scala
index 723adcc45a7..b7289d44a9a 100644
--- a/hail/hail/src/is/hail/backend/spark/SparkBackend.scala
+++ b/hail/hail/src/is/hail/backend/spark/SparkBackend.scala
@@ -4,6 +4,7 @@ import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend._
 import is.hail.backend.Backend.PartitionFn
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Validate
 import is.hail.expr.ir._
 import is.hail.expr.ir.analyses.SemanticHash
@@ -14,7 +15,6 @@ import is.hail.rvd.RVD
 import is.hail.types._
 import is.hail.types.physical.{PStruct, PTuple}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 import scala.concurrent.{CancellationException, ExecutionException}
@@ -32,7 +32,7 @@ import org.apache.spark.sql.SparkSession
 import sourcecode.Enclosing
 
 class SparkBroadcastValue[T](bc: Broadcast[T]) extends BroadcastValue[T] with Serializable {
-  def value: T = bc.value
+  override def value: T = bc.value
 }
 
 object SparkTaskContext {
@@ -109,7 +109,7 @@ object SparkBackend extends Logging {
     : SparkConf = {
     require(blockSize >= 0)
 
-    checkSparkCompatibility(is.hail.HAIL_SPARK_VERSION, org.apache.spark.SPARK_VERSION)
+    checkSparkCompatibility(is.hail.SparkVersion, org.apache.spark.SPARK_VERSION)
 
     val conf = new SparkConf().setAppName(appName)
 
@@ -231,7 +231,7 @@ class SparkBackend(val spark: SparkSession) extends Backend with Logging {
   val sc: SparkContext =
     spark.sparkContext
 
-  def broadcast[T: ClassTag](value: T): BroadcastValue[T] =
+  override def broadcast[T: ClassTag](value: T): BroadcastValue[T] =
     new SparkBroadcastValue[T](sc.broadcast(value))
 
   override def runtimeContext(ctx: ExecuteContext): DriverRuntimeContext =
@@ -316,12 +316,12 @@ class SparkBackend(val spark: SparkSession) extends Backend with Logging {
       }
     }
 
-  def defaultParallelism: Int =
+  override def defaultParallelism: Int =
     sc.defaultParallelism
 
   override def asSpark(implicit E: Enclosing): SparkBackend = this
 
-  def close(): Unit =
+  override def close(): Unit =
     SparkBackend.synchronized {
       assert(this eq SparkBackend.theSparkBackend)
       SparkBackend.theSparkBackend = null
@@ -424,7 +424,7 @@ class SparkBackend(val spark: SparkSession) extends Backend with Logging {
     RVDTableReader(RVD.unkeyed(rowPType, orderedCRDD), globalsLit, rt)
   }
 
-  def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
+  override def tableToTableStage(ctx: ExecuteContext, inputIR: TableIR, analyses: LoweringAnalyses)
     : TableStage =
     CanLowerEfficiently(ctx, inputIR) match {
       case Some(failReason) =>
diff --git a/hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala b/hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala
index 95d595ac6b0..d412782cd99 100644
--- a/hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala
+++ b/hail/hail/src/is/hail/compatibility/LegacyBufferSpecs.scala
@@ -6,7 +6,7 @@ import is.hail.io.compress.LZ4
 
 final case class LZ4BlockBufferSpec(blockSize: Int, child: BlockBufferSpec)
     extends LZ4BlockBufferSpecCommon {
-  def lz4 = LZ4.hc
-  def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "hc")
-  def typeName = "LZ4BlockBufferSpec"
+  override def lz4 = LZ4.hc
+  override def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "hc")
+  override def typeName = "LZ4BlockBufferSpec"
 }
diff --git a/hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala b/hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala
index a8168a86a84..aa6f7e3cc61 100644
--- a/hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala
+++ b/hail/hail/src/is/hail/compatibility/LegacyEncodedTypeParser.scala
@@ -1,10 +1,10 @@
 package is.hail.compatibility
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{IRParser, PunctuationToken, TokenIterator}
 import is.hail.expr.ir.IRParser._
 import is.hail.types.encoded._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object LegacyEncodedTypeParser {
 
diff --git a/hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala b/hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala
index 26366b0293f..527a672b044 100644
--- a/hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala
+++ b/hail/hail/src/is/hail/compatibility/LegacyRVDSpecs.scala
@@ -1,12 +1,13 @@
 package is.hail.compatibility
 
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.io._
 import is.hail.rvd.{AbstractRVDSpec, IndexSpec2, IndexedRVDSpec2, RVDPartitioner}
 import is.hail.types.encoded._
 import is.hail.types.virtual._
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.utils.Interval
 
 import org.json4s.JValue
 
@@ -109,7 +110,7 @@ trait ShimRVDSpec extends AbstractRVDSpec {
 
   val shim: AbstractRVDSpec
 
-  final def key: IndexedSeq[String] = shim.key
+  final override def key: IndexedSeq[String] = shim.key
 
   override def partitioner(sm: HailStateManager): RVDPartitioner = shim.partitioner(sm)
 
@@ -148,12 +149,12 @@ case class UnpartitionedRVDSpec private (
 ) extends AbstractRVDSpec {
   private val (rowVType: TStruct, rowEType) = LegacyEncodedTypeParser.parseTypeAndEType(rowType)
 
-  def partitioner(sm: HailStateManager): RVDPartitioner =
+  override def partitioner(sm: HailStateManager): RVDPartitioner =
     RVDPartitioner.unkeyed(sm, partFiles.length)
 
-  def key: IndexedSeq[String] = FastSeq()
+  override def key: IndexedSeq[String] = FastSeq()
 
-  def typedCodecSpec: AbstractTypedCodecSpec =
+  override def typedCodecSpec: AbstractTypedCodecSpec =
     TypedCodecSpec(rowEType.setRequired(true), rowVType, codecSpec.child)
 
   val attrs: Map[String, String] = Map.empty
@@ -167,9 +168,9 @@ case class OrderedRVDSpec private (
 ) extends AbstractRVDSpec {
   private val lRvdType = LegacyEncodedTypeParser.parseLegacyRVDType(rvdType)
 
-  def key: IndexedSeq[String] = lRvdType.key
+  override def key: IndexedSeq[String] = lRvdType.key
 
-  def partitioner(sm: HailStateManager): RVDPartitioner = {
+  override def partitioner(sm: HailStateManager): RVDPartitioner = {
     val rangeBoundsType = TArray(TInterval(lRvdType.keyType))
     new RVDPartitioner(
       sm,
diff --git a/hail/hail/src/is/hail/cxx/RegionValueIterator.scala b/hail/hail/src/is/hail/cxx/RegionValueIterator.scala
index 9b4cc37f4cd..d5c1ff22760 100644
--- a/hail/hail/src/is/hail/cxx/RegionValueIterator.scala
+++ b/hail/hail/src/is/hail/cxx/RegionValueIterator.scala
@@ -4,7 +4,7 @@ import is.hail.annotations.RegionValue
 
 class RegionValueIterator(it: Iterator[RegionValue]) extends Iterator[Long] {
 
-  def next(): Long = it.next().offset
+  override def next(): Long = it.next().offset
 
-  def hasNext: Boolean = it.hasNext
+  override def hasNext: Boolean = it.hasNext
 }
diff --git a/hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala b/hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala
index e19680bbdc7..ff2c891ece8 100644
--- a/hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala
+++ b/hail/hail/src/is/hail/experimental/ExperimentalFunctions.scala
@@ -8,7 +8,7 @@ import is.hail.types.virtual.{TArray, TFloat64, TInt32, Type}
 
 object ExperimentalFunctions extends RegistryFunctions {
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     val experimentalPackageClass = Class.forName("is.hail.experimental.package$")
 
     registerScalaFunction(
diff --git a/hail/hail/src/is/hail/experimental/package.scala b/hail/hail/src/is/hail/experimental/package.scala
index 01981d41ad3..8c963e52b4b 100644
--- a/hail/hail/src/is/hail/experimental/package.scala
+++ b/hail/hail/src/is/hail/experimental/package.scala
@@ -1,7 +1,8 @@
 package is.hail
 
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.stats._
-import is.hail.utils._
 
 import breeze.linalg.{max, sum, DenseVector}
 import breeze.numerics._
@@ -55,7 +56,7 @@ package object experimental {
 
     // Needs some non-ref samples to compute
     if (_gtCounts(0) >= nSamples) {
-      return FastSeq(_gtCounts(0).toDouble, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
+      return FastSeq(_gtCounts(0).toDouble, 0.0, 0.0, 0.0)
     }
 
     val nHaplotypes = 2.0 * nSamples.toDouble
@@ -91,7 +92,7 @@ package object experimental {
 
     }
 
-    return (p_next *:* nHaplotypes).toArray.toFastSeq
+    (p_next *:* nHaplotypes).toArray.toFastSeq
   }
 
 }
diff --git a/hail/hail/src/is/hail/expr/Parser.scala b/hail/hail/src/is/hail/expr/Parser.scala
index 24e234507a1..8d764ec38ac 100644
--- a/hail/hail/src/is/hail/expr/Parser.scala
+++ b/hail/hail/src/is/hail/expr/Parser.scala
@@ -86,7 +86,7 @@ object Parser extends JavaTokenParsers {
   def oneOfLiteral(a: IndexedSeq[String]): Parser[String] = new Parser[String] {
     private[this] val root = ParseTrieNode.generate(a)
 
-    def apply(in: Input): ParseResult[String] = {
+    override def apply(in: Input): ParseResult[String] = {
 
       var _in = in
       var node = root
diff --git a/hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala b/hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala
index e1fcbae7dbb..1f0d3841a35 100644
--- a/hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala
+++ b/hail/hail/src/is/hail/expr/ir/AbstractMatrixTableSpec.scala
@@ -1,5 +1,6 @@
 package is.hail.expr.ir
 
+import is.hail.collection.FastSeq
 import is.hail.io.fs.FS
 import is.hail.rvd._
 import is.hail.types.virtual.{MatrixType, MatrixTypeSerializer, TableType, TableTypeSerializer}
@@ -154,7 +155,7 @@ abstract class AbstractMatrixTableSpec extends RelationalSpec {
 
   def entriesSpec: AbstractTableSpec
 
-  def indexed: Boolean = rowsSpec.indexed
+  override def indexed: Boolean = rowsSpec.indexed
 }
 
 object MatrixTableSpec {
@@ -219,17 +220,17 @@ class MatrixTableSpec(
   val rowsSpec: AbstractTableSpec,
   val entriesSpec: AbstractTableSpec,
 ) extends AbstractMatrixTableSpec {
-  def references_rel_path: String = params.references_rel_path
+  override def references_rel_path: String = params.references_rel_path
 
-  def file_version: Int = params.file_version
+  override def file_version: Int = params.file_version
 
-  def hail_version: String = params.hail_version
+  override def hail_version: String = params.hail_version
 
-  def matrix_type: MatrixType = params.matrix_type
+  override def matrix_type: MatrixType = params.matrix_type
 
-  def components: Map[String, ComponentSpec] = params.components
+  override def components: Map[String, ComponentSpec] = params.components
 
-  def toJValue: JValue =
+  override def toJValue: JValue =
     decomposeWithName(params, "MatrixTableSpec")(RelationalSpec.formats)
 }
 
diff --git a/hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala b/hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala
index 4bf3e1f9205..eaa382c95d5 100644
--- a/hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala
+++ b/hail/hail/src/is/hail/expr/ir/AbstractTableSpec.scala
@@ -29,13 +29,13 @@ sealed abstract class SortOrder {
 }
 
 case object Ascending extends SortOrder {
-  def serialize: Byte = 0.toByte
-  def parsableString(): String = "A"
+  override def serialize: Byte = 0.toByte
+  override def parsableString(): String = "A"
 }
 
 case object Descending extends SortOrder {
-  def serialize: Byte = 1.toByte
-  def parsableString(): String = "D"
+  override def serialize: Byte = 1.toByte
+  override def parsableString(): String = "D"
 }
 
 object SortField {
@@ -59,7 +59,7 @@ abstract class AbstractTableSpec extends RelationalSpec {
 
   def globalsSpec: AbstractRVDSpec
 
-  def indexed: Boolean = rowsSpec.indexed
+  override def indexed: Boolean = rowsSpec.indexed
 }
 
 object TableSpec {
@@ -99,16 +99,16 @@ class TableSpec(
   val globalsSpec: AbstractRVDSpec,
   val rowsSpec: AbstractRVDSpec,
 ) extends AbstractTableSpec {
-  def file_version: Int = params.file_version
+  override def file_version: Int = params.file_version
 
-  def hail_version: String = params.hail_version
+  override def hail_version: String = params.hail_version
 
-  def components: Map[String, ComponentSpec] = params.components
+  override def components: Map[String, ComponentSpec] = params.components
 
-  def references_rel_path: String = params.references_rel_path
+  override def references_rel_path: String = params.references_rel_path
 
-  def table_type: TableType = params.table_type
+  override def table_type: TableType = params.table_type
 
-  def toJValue: JValue =
+  override def toJValue: JValue =
     decomposeWithName(params, "TableSpec")(RelationalSpec.formats)
 }
diff --git a/hail/hail/src/is/hail/expr/ir/AggOp.scala b/hail/hail/src/is/hail/expr/ir/AggOp.scala
index 85864ae797e..ebc5885ebf9 100644
--- a/hail/hail/src/is/hail/expr/ir/AggOp.scala
+++ b/hail/hail/src/is/hail/expr/ir/AggOp.scala
@@ -1,8 +1,8 @@
 package is.hail.expr.ir
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.agg._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 sealed trait AggOp {}
 final case class ApproxCDF() extends AggOp
diff --git a/hail/hail/src/is/hail/expr/ir/ArraySorter.scala b/hail/hail/src/is/hail/expr/ir/ArraySorter.scala
index 3267f0913d6..2a290c07e31 100644
--- a/hail/hail/src/is/hail/expr/ir/ArraySorter.scala
+++ b/hail/hail/src/is/hail/expr/ir/ArraySorter.scala
@@ -2,14 +2,13 @@ package is.hail.expr.ir
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.types.physical.{PCanonicalArray, PCanonicalDict, PCanonicalSet}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
 import is.hail.types.virtual.{TArray, TDict, TSet, Type}
-import is.hail.utils.FastSeq
 
-class ArraySorter(r: EmitRegion, array: StagedArrayBuilder) {
+class ArraySorter(mb: EmitMethodBuilder[_], r: Value[Region], array: StagedArrayBuilder) {
   val ti: TypeInfo[_] = array.elt.ti
-  val mb: EmitMethodBuilder[_] = r.mb
 
   private[this] var prunedMissing: Boolean = false
 
@@ -191,8 +190,8 @@ class ArraySorter(r: EmitRegion, array: StagedArrayBuilder) {
           array.elt.loadedSType.storageType().setRequired(this.prunedMissing || array.eltRequired)
         )
 
-        arrayType.constructFromElements(cb, r.region, len, deepCopy = false) { (cb, idx) =>
-          array.loadFromIndex(cb, r.region, idx)
+        arrayType.constructFromElements(cb, r, len, deepCopy = false) { (cb, idx) =>
+          array.loadFromIndex(cb, r, idx)
         }
       case td: TDict =>
         PCanonicalDict.coerceArrayCode(toRegion(cb, TArray(td.elementType)))
diff --git a/hail/hail/src/is/hail/expr/ir/BaseIR.scala b/hail/hail/src/is/hail/expr/ir/BaseIR.scala
index 1be2436ba9e..20f63254f38 100644
--- a/hail/hail/src/is/hail/expr/ir/BaseIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/BaseIR.scala
@@ -1,8 +1,8 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.implicits.toRichIndexedSeqAnyRef
 import is.hail.types.virtual.{Type, VType}
-import is.hail.utils._
 import is.hail.utils.StackSafe._
 
 case class Name(str: String) {
diff --git a/hail/hail/src/is/hail/expr/ir/BinarySearch.scala b/hail/hail/src/is/hail/expr/ir/BinarySearch.scala
index aa99b6cbee7..e24be92eadf 100644
--- a/hail/hail/src/is/hail/expr/ir/BinarySearch.scala
+++ b/hail/hail/src/is/hail/expr/ir/BinarySearch.scala
@@ -1,10 +1,10 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.orderings.CodeOrdering
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces._
-import is.hail.utils.FastSeq
 
 object BinarySearch {
   object Comparator {
@@ -12,7 +12,7 @@ object BinarySearch {
       ltNeedle: IEmitCode => Code[Boolean],
       gtNeedle: IEmitCode => Code[Boolean],
     ): Comparator = new Comparator {
-      def apply(
+      override def apply(
         cb: EmitCodeBuilder,
         elt: IEmitCode,
         ifLtNeedle: => Unit,
@@ -29,7 +29,7 @@ object BinarySearch {
     }
 
     def fromCompare(compare: IEmitCode => Value[Int]): Comparator = new Comparator {
-      def apply(
+      override def apply(
         cb: EmitCodeBuilder,
         elt: IEmitCode,
         ifLtNeedle: => Unit,
@@ -42,7 +42,7 @@ object BinarySearch {
     }
 
     def fromPred(pred: IEmitCode => Code[Boolean]): Comparator = new Comparator {
-      def apply(
+      override def apply(
         cb: EmitCodeBuilder,
         elt: IEmitCode,
         ifLtNeedle: => Unit,
diff --git a/hail/hail/src/is/hail/expr/ir/Binds.scala b/hail/hail/src/is/hail/expr/ir/Binds.scala
index d7fe71f2a1a..30fd3a52736 100644
--- a/hail/hail/src/is/hail/expr/ir/Binds.scala
+++ b/hail/hail/src/is/hail/expr/ir/Binds.scala
@@ -1,10 +1,10 @@
 package is.hail.expr.ir
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs._
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
 import is.hail.types.virtual.TIterable.elementType
-import is.hail.utils.FastSeq
 
 import scala.collection.mutable
 
diff --git a/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala
index 6f964bdce49..701e6bb3f62 100644
--- a/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/BlockMatrixIR.scala
@@ -2,17 +2,18 @@ package is.hail.expr.ir
 
 import is.hail.annotations.NDArray
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.lowering.{BMSContexts, BlockMatrixStage2, LowererUnsupportedOperation}
-import is.hail.io.{StreamBufferSpec, TypedCodecSpec}
+import is.hail.io.TypedCodecSpec
 import is.hail.io.fs.FS
 import is.hail.linalg.{BlockMatrix, BlockMatrixMetadata, MatrixSparsity}
-import is.hail.types.encoded.{EBlockMatrixNDArray, EFloat64, ENumpyBinaryNDArray}
+import is.hail.linalg.implicits.RichDenseMatrixDouble
+import is.hail.types.encoded.{EBlockMatrixNDArray, EFloat64}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.richUtils.RichDenseMatrixDouble
 
 import scala.collection.immutable.NumericRange
 import scala.collection.mutable.ArrayBuffer
@@ -46,7 +47,7 @@ object BlockMatrixIR {
 }
 
 sealed abstract class BlockMatrixIR extends BaseIR {
-  def typ: BlockMatrixType
+  override def typ: BlockMatrixType
 
   protected[ir] def execute(ctx: ExecuteContext): BlockMatrix =
     fatal("tried to execute unexecutable IR:\n" + Pretty(ctx, this))
@@ -126,7 +127,7 @@ class BlockMatrixNativeReader(
   val params: BlockMatrixNativeReaderParameters,
   val metadata: BlockMatrixMetadata,
 ) extends BlockMatrixReader {
-  def pathsUsed: Seq[String] = Array(params.path)
+  override def pathsUsed: Seq[String] = Array(params.path)
 
   lazy val fullType: BlockMatrixType = {
     val sparsity = MatrixSparsity.fromLinearCoords(
@@ -137,7 +138,7 @@ class BlockMatrixNativeReader(
     BlockMatrixType(TFloat64, metadata.nRows, metadata.nCols, metadata.blockSize, sparsity)
   }
 
-  def apply(ctx: ExecuteContext): BlockMatrix = {
+  override def apply(ctx: ExecuteContext): BlockMatrix = {
     val key = ("BlockMatrixNativeReader.apply", params.path)
     if (ctx.memo.contains(key)) {
       ctx.memo(key).asInstanceOf[BlockMatrix]
@@ -195,7 +196,7 @@ class BlockMatrixNativeReader(
 
 case class BlockMatrixBinaryReader(path: String, shape: IndexedSeq[Long], blockSize: Int)
     extends BlockMatrixReader {
-  def pathsUsed: Seq[String] = Array(path)
+  override def pathsUsed: Seq[String] = Array(path)
 
   val IndexedSeq(nRows, nCols) = shape
   BlockMatrixIR.checkFitsIntoArray(nRows, nCols)
@@ -203,7 +204,7 @@ case class BlockMatrixBinaryReader(path: String, shape: IndexedSeq[Long], blockS
   lazy val fullType: BlockMatrixType =
     BlockMatrixType.dense(TFloat64, nRows, nCols, blockSize)
 
-  def apply(ctx: ExecuteContext): BlockMatrix = {
+  override def apply(ctx: ExecuteContext): BlockMatrix = {
     val breezeMatrix =
       RichDenseMatrixDouble.importFromDoubles(
         ctx.fs,
@@ -216,11 +217,7 @@ case class BlockMatrixBinaryReader(path: String, shape: IndexedSeq[Long], blockS
   }
 
   override def lower(ctx: ExecuteContext, evalCtx: IRBuilder): BlockMatrixStage2 = {
-    // FIXME numpy should be it's own value reader
-    val readFromNumpyEType = ENumpyBinaryNDArray(nRows, nCols, true)
-    val readFromNumpySpec =
-      TypedCodecSpec(readFromNumpyEType, TNDArray(TFloat64, Nat(2)), new StreamBufferSpec())
-    val reader = ETypeValueReader(readFromNumpySpec)
+    val reader = NumpyBinaryValueReader(nRows, nCols)
     val nd = evalCtx.memoize(ReadValue(Str(path), reader, TNDArray(TFloat64, nDimsBase = Nat(2))))
 
     val typ = fullType
@@ -262,9 +259,9 @@ object BlockMatrixPersistReader {
 }
 
 case class BlockMatrixPersistReader(id: String, typ: BlockMatrixType) extends BlockMatrixReader {
-  def pathsUsed: Seq[String] = FastSeq()
+  override def pathsUsed: Seq[String] = FastSeq()
   lazy val fullType: BlockMatrixType = typ
-  def apply(ctx: ExecuteContext): BlockMatrix = ctx.BlockMatrixCache(id)
+  override def apply(ctx: ExecuteContext): BlockMatrix = ctx.BlockMatrixCache(id)
 }
 
 case class BlockMatrixMap(child: BlockMatrixIR, eltName: Name, f: IR, needsDense: Boolean)
@@ -372,23 +369,23 @@ abstract class SparsityStrategy {
 }
 
 case object UnionBlocks extends SparsityStrategy {
-  def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = leftBlock || rightBlock
+  override def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = leftBlock || rightBlock
 
-  def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity =
+  override def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity =
     MatrixSparsity.union(left, right)
 }
 
 case object IntersectionBlocks extends SparsityStrategy {
-  def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = leftBlock && rightBlock
+  override def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = leftBlock && rightBlock
 
-  def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity =
+  override def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity =
     MatrixSparsity.intersection(left, right)
 }
 
 case object NeedsDense extends SparsityStrategy {
-  def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = true
+  override def exists(leftBlock: Boolean, rightBlock: Boolean): Boolean = true
 
-  def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity = {
+  override def mergeSparsity(left: MatrixSparsity, right: MatrixSparsity): MatrixSparsity = {
     assert(left.nRows == right.nRows && left.nCols == right.nCols)
     assert(!left.isSparse && !right.isSparse)
     left
@@ -786,7 +783,7 @@ case class BlockMatrixFilter(
 case class BlockMatrixDensify(child: BlockMatrixIR) extends BlockMatrixIR {
   override lazy val typ: BlockMatrixType = child.typ.densify
 
-  def blockCostIsLinear: Boolean = child.blockCostIsLinear
+  override def blockCostIsLinear: Boolean = child.blockCostIsLinear
 
   val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
 
@@ -810,7 +807,7 @@ sealed abstract class BlockMatrixSparsifier {
 case class BandSparsifier(blocksOnly: Boolean, l: Long, u: Long) extends BlockMatrixSparsifier {
   val typ: Type = TTuple(TInt64, TInt64)
 
-  def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
+  override def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
     val lowerBlock = java.lang.Math.floorDiv(l, childType.blockSize).toInt
     val upperBlock = java.lang.Math.floorDiv(u + childType.blockSize - 1, childType.blockSize).toInt
 
@@ -830,7 +827,7 @@ case class BandSparsifier(blocksOnly: Boolean, l: Long, u: Long) extends BlockMa
   override def sparsify(ctx: ExecuteContext, bm: BlockMatrix): BlockMatrix =
     bm.filterBand(l, u, blocksOnly)
 
-  def pretty(): String =
+  override def pretty(): String =
     s"(BandSparsifier ${Pretty.prettyBooleanLiteral(blocksOnly)} $l $u)"
 }
 
@@ -842,7 +839,7 @@ case class RowIntervalSparsifier(
 ) extends BlockMatrixSparsifier {
   val typ: Type = TTuple(TArray(TInt64), TArray(TInt64))
 
-  def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
+  override def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
     val blockStarts =
       starts.grouped(childType.blockSize).map(idxs => childType.getBlockIdx(idxs.min)).toArray
     val blockStops =
@@ -856,7 +853,7 @@ case class RowIntervalSparsifier(
   override def sparsify(ctx: ExecuteContext, bm: BlockMatrix): BlockMatrix =
     bm.filterRowIntervals(ctx, starts.toArray, stops.toArray, blocksOnly)
 
-  def pretty(): String =
+  override def pretty(): String =
     s"(RowIntervalSparsifier ${Pretty.prettyBooleanLiteral(blocksOnly)} ${starts.mkString("(", " ", ")")} ${stops.mkString("(", " ", ")")})"
 }
 
@@ -865,7 +862,7 @@ case class RectangleSparsifier(rectangles: IndexedSeq[IndexedSeq[Long]])
     extends BlockMatrixSparsifier {
   val typ: Type = TArray(TInt64)
 
-  def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
+  override def definedBlocks(childType: BlockMatrixType): MatrixSparsity = {
     val definedBlocks = rectangles.flatMap { case IndexedSeq(rowStart, rowEnd, colStart, colEnd) =>
       val rs = childType.getBlockIdx(java.lang.Math.max(rowStart, 0))
       val re = childType.getBlockIdx(java.lang.Math.min(rowEnd - 1, childType.nRows)) + 1
@@ -884,7 +881,7 @@ case class RectangleSparsifier(rectangles: IndexedSeq[IndexedSeq[Long]])
   override def sparsify(ctx: ExecuteContext, bm: BlockMatrix): BlockMatrix =
     bm.filterRectangles(rectangles.flatten.toArray)
 
-  def pretty(): String =
+  override def pretty(): String =
     s"(RectangleSparsifier ${rectangles.flatten.mkString("(", " ", ")")})"
 }
 
@@ -912,7 +909,7 @@ case class BlockMatrixSparsify(
   override lazy val typ: BlockMatrixType =
     child.typ.copy(sparsity = sparsifier.definedBlocks(child.typ))
 
-  def blockCostIsLinear: Boolean = child.blockCostIsLinear
+  override def blockCostIsLinear: Boolean = child.blockCostIsLinear
 
   val childrenSeq: IndexedSeq[BaseIR] = Array(child)
 
diff --git a/hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala b/hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala
index f44f90b1f7e..407f13736dd 100644
--- a/hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala
+++ b/hail/hail/src/is/hail/expr/ir/BlockMatrixWriter.scala
@@ -6,14 +6,14 @@ import is.hail.backend.ExecuteContext
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs.{MetadataWriter, Str, UUID4, WriteMetadata, WriteValue}
 import is.hail.expr.ir.lowering.{BlockMatrixStage2, LowererUnsupportedOperation}
-import is.hail.io.{StreamBufferSpec, TypedCodecSpec}
+import is.hail.io.TypedCodecSpec
 import is.hail.io.fs.FS
 import is.hail.linalg.{BlockMatrix, BlockMatrixMetadata, MatrixSparsity}
+import is.hail.linalg.implicits.RichDenseMatrixDouble
 import is.hail.types.TypeWithRequiredness
-import is.hail.types.encoded.{EBlockMatrixNDArray, ENumpyBinaryNDArray, EType}
+import is.hail.types.encoded.{EBlockMatrixNDArray, EType}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.richUtils.RichDenseMatrixDouble
 
 import java.io.DataOutputStream
 
@@ -56,12 +56,12 @@ case class BlockMatrixNativeWriter(
   forceRowMajor: Boolean,
   stageLocally: Boolean,
 ) extends BlockMatrixWriter {
-  def pathOpt: Option[String] = Some(path)
+  override def pathOpt: Option[String] = Some(path)
 
-  def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
+  override def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
     bm.write(ctx, path, overwrite, forceRowMajor, stageLocally)
 
-  def loweredTyp: Type = TVoid
+  override def loweredTyp: Type = TVoid
 
   override def lower(
     ctx: ExecuteContext,
@@ -110,7 +110,7 @@ case class BlockMatrixNativeMetadataWriter(
     def write(fs: FS, rawPartFiles: Array[String]): Unit = {
       val partFiles = rawPartFiles.map(_.split('/').last)
       using(new DataOutputStream(fs.create(s"$path/metadata.json"))) { os =>
-        implicit val formats = defaultJSONFormats
+        implicit val formats = DefaultFormats
         jackson.Serialization.write(
           BlockMatrixMetadata(blockSize, nRows, nCols, partIdxToBlockIdx, partFiles),
           os,
@@ -128,9 +128,9 @@ case class BlockMatrixNativeMetadataWriter(
     }
   }
 
-  def annotationType: Type = TArray(TString)
+  override def annotationType: Type = TArray(TString)
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -164,9 +164,9 @@ case class BlockMatrixNativeMetadataWriter(
 }
 
 case class BlockMatrixBinaryWriter(path: String) extends BlockMatrixWriter {
-  def pathOpt: Option[String] = Some(path)
+  override def pathOpt: Option[String] = Some(path)
 
-  def apply(ctx: ExecuteContext, bm: BlockMatrix): String = {
+  override def apply(ctx: ExecuteContext, bm: BlockMatrix): String = {
     RichDenseMatrixDouble.exportToDoubles(
       ctx.fs,
       path,
@@ -176,7 +176,7 @@ case class BlockMatrixBinaryWriter(path: String) extends BlockMatrixWriter {
     path
   }
 
-  def loweredTyp: Type = TString
+  override def loweredTyp: Type = TString
 
   override def lower(
     ctx: ExecuteContext,
@@ -185,22 +185,18 @@ case class BlockMatrixBinaryWriter(path: String) extends BlockMatrixWriter {
     eltR: TypeWithRequiredness,
   ): IR = {
     val nd = s.collectLocal(evalCtx, "block_matrix_binary_writer")
-
-    // FIXME remove numpy encoder
-    val etype = ENumpyBinaryNDArray(s.typ.nRows, s.typ.nCols, true)
-    val spec = TypedCodecSpec(etype, TNDArray(s.typ.elementType, Nat(2)), new StreamBufferSpec())
-    val writer = ETypeValueWriter(spec)
+    val writer = NumpyBinaryValueWriter(s.typ.nRows, s.typ.nCols)
     WriteValue(nd, Str(path), writer)
   }
 }
 
 case class BlockMatrixPersistWriter(id: String, storageLevel: String) extends BlockMatrixWriter {
-  def pathOpt: Option[String] = None
+  override def pathOpt: Option[String] = None
 
-  def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
+  override def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
     ctx.BlockMatrixCache += id -> bm.persist(storageLevel)
 
-  def loweredTyp: Type = TVoid
+  override def loweredTyp: Type = TVoid
 }
 
 case class BlockMatrixRectanglesWriter(
@@ -210,12 +206,12 @@ case class BlockMatrixRectanglesWriter(
   binary: Boolean,
 ) extends BlockMatrixWriter {
 
-  def pathOpt: Option[String] = Some(path)
+  override def pathOpt: Option[String] = Some(path)
 
-  def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
+  override def apply(ctx: ExecuteContext, bm: BlockMatrix): Unit =
     bm.exportRectangles(ctx, path, rectangles, delimiter, binary)
 
-  def loweredTyp: Type = TVoid
+  override def loweredTyp: Type = TVoid
 }
 
 abstract class BlockMatrixMultiWriter {
@@ -227,7 +223,7 @@ case class BlockMatrixBinaryMultiWriter(
   overwrite: Boolean,
 ) extends BlockMatrixMultiWriter {
 
-  def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
+  override def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
     BlockMatrix.binaryWriteBlockMatrices(ctx, bms, prefix, overwrite)
 
   def loweredTyp: Type = TVoid
@@ -243,7 +239,7 @@ case class BlockMatrixTextMultiWriter(
   customFilenames: Option[Array[String]],
 ) extends BlockMatrixMultiWriter {
 
-  def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
+  override def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
     BlockMatrix.exportBlockMatrices(
       ctx,
       bms,
@@ -265,7 +261,7 @@ case class BlockMatrixNativeMultiWriter(
   forceRowMajor: Boolean,
 ) extends BlockMatrixMultiWriter {
 
-  def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
+  override def apply(ctx: ExecuteContext, bms: IndexedSeq[BlockMatrix]): Unit =
     BlockMatrix.writeBlockMatrices(ctx, bms, prefix, overwrite, forceRowMajor)
 
   def loweredTyp: Type = TVoid
diff --git a/hail/hail/src/is/hail/expr/ir/Compilable.scala b/hail/hail/src/is/hail/expr/ir/Compilable.scala
index d03fd6cb37e..767b84e4350 100644
--- a/hail/hail/src/is/hail/expr/ir/Compilable.scala
+++ b/hail/hail/src/is/hail/expr/ir/Compilable.scala
@@ -4,7 +4,6 @@ import is.hail.expr.ir.defs._
 
 object InterpretableButNotCompilable {
   def apply(x: IR): Boolean = x match {
-    case _: LiftMeOut => true
     case _: TableCount => true
     case _: TableGetGlobals => true
     case _: TableCollect => true
diff --git a/hail/hail/src/is/hail/expr/ir/Compile.scala b/hail/hail/src/is/hail/expr/ir/Compile.scala
index 2a3b6369904..ed9a83dfda7 100644
--- a/hail/hail/src/is/hail/expr/ir/Compile.scala
+++ b/hail/hail/src/is/hail/expr/ir/Compile.scala
@@ -3,6 +3,8 @@ package is.hail.expr.ir
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailTaskContext}
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.agg.AggStateSig
 import is.hail.expr.ir.defs.In
 import is.hail.expr.ir.lowering.LoweringPipeline
@@ -14,8 +16,6 @@ import is.hail.types.physical.stypes.{
   PTypeReferenceSingleCodeType, SingleCodeType, StreamSingleCodeType,
 }
 import is.hail.types.physical.stypes.interfaces.{NoBoxLongIterator, SStream}
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import java.io.PrintWriter
 
@@ -23,7 +23,7 @@ import sourcecode.Enclosing
 
 case class CodeCacheKey(
   aggSigs: IndexedSeq[AggStateSig],
-  args: Seq[(Name, EmitParamType)],
+  args: Seq[EmitParamType],
   body: IR,
 )
 
@@ -90,29 +90,37 @@ object compile {
     N: sourcecode.Name,
   ): (Option[SingleCodeType], (HailClassLoader, FS, HailTaskContext, Region) => F with Mixin) =
     ctx.time {
-      val normalizedBody = NormalizeNames(allowFreeVariables = true)(ctx, body)
-      ctx.CodeCache.getOrElseUpdate(
-        CodeCacheKey(aggSigs.getOrElse(ArraySeq.empty).toFastSeq, params, normalizedBody), {
-          var ir = Subst(
-            body,
+      val ir =
+        NormalizeNames()(
+          ctx,
+          Subst(
+            body.noSharing(ctx),
             BindingEnv(Env.fromSeq(params.zipWithIndex.map { case ((n, t), i) => n -> In(i, t) })),
-          )
-          ir = LoweringPipeline.compileLowerer(ctx, ir).asInstanceOf[IR].noSharing(ctx)
-          TypeCheck(ctx, ir)
-
-          val fb = EmitFunctionBuilder[F](
-            ctx,
-            N.value,
-            CodeParamType(typeInfo[Region]) +: params.map(_._2),
-            CodeParamType(SingleCodeType.typeInfoFromType(ir.typ)),
-            Some("Emit.scala"),
-          )
+          ),
+        )
 
-          /* { def visit(x: IR): Unit = { println(f"${ System.identityHashCode(x) }%08x ${
-           * x.getClass.getSimpleName } ${ x.pType }") Children(x).foreach { case c: IR => visit(c)
-           * } }
-           *
-           * visit(ir) } */
+      val key =
+        CodeCacheKey(
+          aggSigs.getOrElse(IndexedSeq.empty),
+          params.map(_._2),
+          ir,
+        )
+
+      ctx.CodeCache.getOrElseUpdate(
+        key, {
+          val lowered =
+            LoweringPipeline.compileLowerer(ctx, ir)
+              .asInstanceOf[IR]
+              .noSharing(ctx)
+
+          val fb =
+            EmitFunctionBuilder[F](
+              ctx,
+              N.value,
+              CodeParamType(typeInfo[Region]) +: params.map(_._2),
+              CodeParamType(SingleCodeType.typeInfoFromType(lowered.typ)),
+              Some("Emit.scala"),
+            )
 
           assert(
             fb.mb.parameterTypeInfo == expectedCodeParamTypes,
@@ -123,8 +131,8 @@ object compile {
             s"expected $expectedCodeReturnType, got ${fb.mb.returnTypeInfo}",
           )
 
-          val emitContext = EmitContext.analyze(ctx, ir)
-          val rt = Emit(emitContext, ir, fb, expectedCodeReturnType, params.length, aggSigs)
+          val emitContext = EmitContext.analyze(ctx, lowered)
+          val rt = Emit(emitContext, lowered, fb, expectedCodeReturnType, params.length, aggSigs)
           CompiledFunction(rt, fb.resultWithIndex(print))
         },
       ).asInstanceOf[CompiledFunction[F with Mixin]].tuple
@@ -156,7 +164,7 @@ object CompileIterator {
     private var _stepped = false
     private var _hasNext = false
 
-    def hasNext: Boolean = {
+    override def hasNext: Boolean = {
       if (!_stepped) {
         _hasNext = step()
         _stepped = true
@@ -164,7 +172,7 @@ object CompileIterator {
       _hasNext
     }
 
-    def next(): java.lang.Long = {
+    override def next(): java.lang.Long = {
       if (!hasNext) Iterator.empty.next(): Unit // throw
       _stepped = false
       stepFunction.loadAddress()
@@ -309,7 +317,7 @@ object CompileIterator {
         new LongIteratorWrapper {
           val stepFunction: TMPStepFunction = outerStepFunction
 
-          def step(): Boolean = stepFunction.apply(null, v0, part)
+          override def step(): Boolean = stepFunction.apply(null, v0, part)
         }
       },
     )
@@ -345,7 +353,7 @@ object CompileIterator {
         new LongIteratorWrapper {
           val stepFunction: TableStageToRVDStepFunction = outerStepFunction
 
-          def step(): Boolean = stepFunction.apply(null, v0, v1)
+          override def step(): Boolean = stepFunction.apply(null, v0, v1)
         }
       },
     )
diff --git a/hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala b/hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala
index 63862efcfd8..2cc11055db9 100644
--- a/hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala
+++ b/hail/hail/src/is/hail/expr/ir/CompileAndEvaluate.scala
@@ -3,13 +3,13 @@ package is.hail.expr.ir
 import is.hail.annotations.{Region, SafeRow}
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs.{Begin, EncodedLiteral, Literal, MakeTuple, NA}
-import is.hail.expr.ir.lowering.{Invariant, LoweringPipeline}
+import is.hail.expr.ir.lowering.LoweringPipeline
 import is.hail.types.physical.PTuple
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import java.io.PrintWriter
 
@@ -49,7 +49,6 @@ object CompileAndEvaluate {
   ): Either[Unit, (PTuple, Long)] =
     ctx.time {
       val ir = lower(ctx, ir0).asInstanceOf[IR]
-      Invariant.CompilableIR.verify(ctx, ir)
 
       ir.typ match {
         case TVoid =>
diff --git a/hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala b/hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala
index 54ad372c06e..68fa24d34d9 100644
--- a/hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala
+++ b/hail/hail/src/is/hail/expr/ir/DeprecatedIRBuilder.scala
@@ -1,8 +1,9 @@
 package is.hail.expr.ir
 
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.defs._
 import is.hail.types.virtual._
-import is.hail.utils.{toRichIterable, FastSeq}
 
 import scala.language.dynamics
 
diff --git a/hail/hail/src/is/hail/expr/ir/Emit.scala b/hail/hail/src/is/hail/expr/ir/Emit.scala
index bdfb6785efc..5cc82a3474d 100644
--- a/hail/hail/src/is/hail/expr/ir/Emit.scala
+++ b/hail/hail/src/is/hail/expr/ir/Emit.scala
@@ -2,7 +2,11 @@ package is.hail.expr.ir
 
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{codeToRichCodeRegion, valueToRichCodeRegion}
 import is.hail.backend.{DriverRuntimeContext, ExecuteContext, HailTaskContext}
+import is.hail.collection.{ByteArrayArrayBuilder, FastSeq}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.agg.{AggStateSig, ArrayAggStateSig, GroupedStateSig}
 import is.hail.expr.ir.analyses.{
   ComputeMethodSplits, ControlFlowPreventsSplit, ParentPointers, SemanticHash,
@@ -68,8 +72,8 @@ case class EmitEnv(bindings: Env[EmitValue], inputValues: IndexedSeq[EmitValue])
 
   def asParams(freeVariables: Env[Unit])
     : (IndexedSeq[ParamType], IndexedSeq[Value[_]], (EmitCodeBuilder, Int) => EmitEnv) = {
-    val m = bindings.m.filterKeys(freeVariables.contains)
-    val bindingNames = m.keys.toArray
+    val m = bindings.m
+    val bindingNames = m.keys.filter(freeVariables.contains).to(ArraySeq)
     val paramTypes =
       bindingNames.map(name => m(name).emitType.paramType) ++ inputValues.map(_.emitType.paramType)
     val params =
@@ -233,14 +237,6 @@ case class AggContainer(
   }
 }
 
-object EmitRegion {
-  def default(mb: EmitMethodBuilder[_]): EmitRegion = EmitRegion(mb, mb.getCodeParam[Region](1))
-}
-
-case class EmitRegion(mb: EmitMethodBuilder[_], region: Value[Region]) {
-  def baseRegion: Value[Region] = mb.getCodeParam[Region](1)
-}
-
 object EmitValue {
   def apply(missing: Option[Value[Boolean]], v: SValue): EmitValue =
     new EmitValue(
@@ -1423,7 +1419,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
 
           val vab = new StagedArrayBuilder(cb, sct, producer.element.required, 0)
           StreamUtils.writeToArrayBuilder(cb, producer, vab, region)
-          val sorter = new ArraySorter(EmitRegion(mb, region), vab)
+          val sorter = new ArraySorter(mb, region, vab)
           sorter.sort(
             cb,
             region,
@@ -1523,7 +1519,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
 
           val vab = new StagedArrayBuilder(cb, sct, producer.element.required, 0)
           StreamUtils.writeToArrayBuilder(cb, producer, vab, region)
-          val sorter = new ArraySorter(EmitRegion(mb, region), vab)
+          val sorter = new ArraySorter(mb, region, vab)
 
           def lessThan(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_])
             : Value[Boolean] =
@@ -1549,7 +1545,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
 
           val vab = new StagedArrayBuilder(cb, sct, producer.element.required, 0)
           StreamUtils.writeToArrayBuilder(cb, producer, vab, region)
-          val sorter = new ArraySorter(EmitRegion(mb, region), vab)
+          val sorter = new ArraySorter(mb, region, vab)
 
           def lessThan(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_])
             : Value[Boolean] = {
@@ -1589,7 +1585,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
           val sct = SingleCodeType.fromSType(producer.element.st)
           val sortedElts = new StagedArrayBuilder(cb, sct, producer.element.required, 16)
           StreamUtils.writeToArrayBuilder(cb, producer, sortedElts, region)
-          val sorter = new ArraySorter(EmitRegion(mb, region), sortedElts)
+          val sorter = new ArraySorter(mb, region, sortedElts)
 
           def lt(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_])
             : Value[Boolean] = {
@@ -1704,7 +1700,8 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
         }
 
       case RNGStateLiteral() =>
-        IEmitCode.present(cb, SRNGStateStaticSizeValue(cb))
+        val state = SRNGStateStaticSizeValue(cb)
+        IEmitCode.present(cb, state)
 
       case RNGSplit(state, dynBitstring) =>
         val stateValue = emitI(state).getOrAssert(cb)
@@ -1724,6 +1721,15 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
         longs.foreach(l => result = result.splitDyn(cb, l))
         presentPC(result)
 
+      case RNGSplitStatic(rngState, staticUid) =>
+        val newState =
+          emitI(rngState)
+            .getOrAssert(cb)
+            .asRNGState
+            .splitStatic(cb, staticUid)
+
+        IEmitCode.present(cb, newState)
+
       case StreamLen(a) =>
         emitStream(a, cb, region).map(cb) { case stream: SStreamValue =>
           val producer = stream.getProducer(mb)
@@ -2497,7 +2503,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
           val M = shapeArray(0)
           val N = shapeArray(1)
           val K = new Value[Long] {
-            def get: Code[Long] = (M < N).mux(M, N)
+            override def get: Code[Long] = (M < N).mux(M, N)
           }
           val LDA = new Value[Long] {
             override def get: Code[Long] =
@@ -2778,22 +2784,6 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
         val rvAgg = agg.Extract.getAgg(sig)
         rvAgg.result(cb, sc.states(idx), region)
 
-      case x @ ApplySeeded(_, args, rngState, staticUID, rt) =>
-        val codeArgs = args.map(a => EmitCode.fromI(cb.emb)(emitInNewBuilder(_, a)))
-        val codeArgsMem = codeArgs.map(_.memoize(cb, "ApplySeeded_arg"))
-        val state = emitI(rngState).getOrAssert(cb)
-        val impl = x.implementation
-        assert(impl.unify(Array.empty[Type], x.argTypes, rt))
-        val newState = EmitCode.present(mb, state.asRNGState.splitStatic(cb, staticUID))
-        impl.applyI(
-          EmitRegion(cb.emb, region),
-          cb,
-          impl.computeReturnEmitType(x.typ, newState.emitType +: codeArgs.map(_.emitType)).st,
-          Seq[Type](),
-          const(0),
-          newState +: codeArgsMem.map(_.load): _*
-        )
-
       case AggStateValue(i, _) =>
         val AggContainer(_, sc, _) = container.get
         presentPC(sc.states(i).serializeToRegion(cb, PCanonicalBinary(), region))
@@ -3541,7 +3531,7 @@ class Emit[C](val ctx: EmitContext, val cb: EmitClassBuilder[C]) {
         val unified = impl.unify(typeArgs, args.map(_.typ), rt)
         assert(unified)
         val retType = impl.computeReturnEmitType(x.typ, codeArgs.map(_.emitType))
-        impl.apply(EmitRegion(mb, region), retType.st, typeArgs, errorID, codeArgs: _*)
+        impl.apply(mb, region, retType.st, typeArgs, errorID, codeArgs: _*)
 
       case WritePartition(stream, pctx, writer) =>
         val ctxCode = emit(pctx)
@@ -3745,7 +3735,7 @@ object NDArrayEmitter {
     val notBroadcasted = 1L
     Array.tabulate(nDims)(dim =>
       new Value[Long] {
-        def get: Code[Long] =
+        override def get: Code[Long] =
           (shapeArray(dim) > 1L).mux(notBroadcasted, broadcasted) * loopVars(dim)
       }
     )
@@ -3756,7 +3746,7 @@ object NDArrayEmitter {
     val notBroadcasted = 1L
     shapeArray.map(shapeElement =>
       new Value[Long] {
-        def get: Code[Long] = (shapeElement > 1L).mux(notBroadcasted, broadcasted)
+        override def get: Code[Long] = (shapeElement > 1L).mux(notBroadcasted, broadcasted)
       }
     )
   }
@@ -3765,7 +3755,7 @@ object NDArrayEmitter {
     : IndexedSeq[Value[Long]] =
     indices.zip(broadcastMask).map { case (index, flag) =>
       new Value[Long] {
-        def get: Code[Long] = index * flag
+        override def get: Code[Long] = index * flag
       }
     }
 
diff --git a/hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala b/hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala
index 3557da46bc4..e30da6fe3a8 100644
--- a/hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala
+++ b/hail/hail/src/is/hail/expr/ir/EmitClassBuilder.scala
@@ -2,9 +2,11 @@ package is.hail.expr.ir
 
 import is.hail.annotations.{Region, RegionPool, RegionValueBuilder}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{codeToRichCodeRegion, valueToRichCodeRegion}
 import is.hail.backend.{BackendUtils, ExecuteContext, HailTaskContext}
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.defs.EncodedLiteral
-import is.hail.expr.ir.functions.IRRandomness
 import is.hail.expr.ir.orderings.{CodeOrdering, StructOrdering}
 import is.hail.io.{BufferSpec, InputBuffer, TypedCodecSpec}
 import is.hail.io.fs.FS
@@ -14,9 +16,7 @@ import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces.SBaseStruct
 import is.hail.types.virtual.Type
 import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.prettyPrint.ArrayOfByteArrayInputStream
+import is.hail.utils.implicits.toRichBoolean
 import is.hail.variant.ReferenceGenome
 
 import scala.collection.mutable
@@ -135,7 +135,7 @@ trait WrappedEmitModuleBuilder {
 trait WrappedEmitClassBuilder[C] extends WrappedEmitModuleBuilder {
   def ecb: EmitClassBuilder[C]
 
-  def emodb: EmitModuleBuilder = ecb.emodb
+  override def emodb: EmitModuleBuilder = ecb.emodb
 
   def cb: ClassBuilder[C] = ecb.cb
 
@@ -248,9 +248,7 @@ trait WrappedEmitClassBuilder[C] extends WrappedEmitModuleBuilder {
   def addAggStates(aggSigs: IndexedSeq[agg.AggStateSig]): agg.TupleAggregatorState =
     ecb.addAggStates(aggSigs)
 
-  def newRNG(seed: Long): Value[IRRandomness] = ecb.newRNG(seed)
-
-  def getThreefryRNG(): Value[ThreefryRandomEngine] = ecb.getThreefryRNG()
+  def threefryRandomEngine: Value[ThreefryRandomEngine] = ecb.threefryRandomEngine
 
   def resultWithIndex(print: Option[PrintWriter] = None)
     : (HailClassLoader, FS, HailTaskContext, Region) => C =
@@ -780,10 +778,6 @@ final class EmitClassBuilder[C](val emodb: EmitModuleBuilder, val cb: ClassBuild
     )
   }
 
-  private val rngs = ArraySeq.newBuilder[(Settable[IRRandomness], Code[IRRandomness])]
-
-  var threefryRNG: Option[(Settable[ThreefryRandomEngine], Code[ThreefryRandomEngine])] = None
-
   def makeAddPartitionRegion(): Unit = {
     cb.addInterface(typeInfo[FunctionWithPartitionRegion].iname)
     val mb =
@@ -852,59 +846,20 @@ final class EmitClassBuilder[C](val emodb: EmitModuleBuilder, val cb: ClassBuild
     }
   }
 
-  def makeRNGs(): Unit = {
-    cb.addInterface(typeInfo[FunctionWithSeededRandomness].iname)
-
-    val initialized = genFieldThisRef[Boolean]("initialized")
-    val mb =
-      newEmitMethod("setPartitionIndex", IndexedSeq[ParamType](typeInfo[Int]), typeInfo[Unit])
-    val rngFields = rngs.result()
-
-    mb.voidWithBuilder { cb =>
-      cb.if_(
-        !initialized, {
-          rngFields.foreach { case (field, init) =>
-            cb.assign(field, init)
-          }
-
-          threefryRNG.foreach { case (field, init) =>
-            cb.assign(field, init)
-          }
-
-          cb.assign(initialized, true)
-        },
+  lazy val threefryRandomEngine: Value[ThreefryRandomEngine] = {
+    val rngField = genFieldThisRef[ThreefryRandomEngine]("threefry")
+    cb.ctor.emitInit {
+      rngField := Code.invokeScalaObject0[ThreefryRandomEngine](
+        ThreefryRandomEngine.getClass,
+        "apply",
       )
-
-      rngFields.foreach { case (field, _) =>
-        cb += field.invoke[Int, Unit]("reset", mb.getCodeParam[Int](1))
-      }
-    }
-  }
-
-  def newRNG(seed: Long): Value[IRRandomness] = {
-    val rng = genFieldThisRef[IRRandomness]()
-    rngs += rng -> Code.newInstance[IRRandomness, Long](seed)
-    rng
-  }
-
-  def getThreefryRNG(): Value[ThreefryRandomEngine] = {
-    threefryRNG match {
-      case Some((rngField, _)) => rngField
-      case None =>
-        val rngField = genFieldThisRef[ThreefryRandomEngine]()
-        val rngInit = Code.invokeScalaObject0[ThreefryRandomEngine](
-          ThreefryRandomEngine.getClass,
-          "apply",
-        )
-        threefryRNG = Some(rngField -> rngInit)
-        rngField
     }
+    rngField
   }
 
   def resultWithIndex(print: Option[PrintWriter] = None)
     : (HailClassLoader, FS, HailTaskContext, Region) => C =
     ctx.time {
-      makeRNGs()
       makeAddPartitionRegion()
       makeAddHailClassLoader()
       makeAddFS()
@@ -944,7 +899,8 @@ final class EmitClassBuilder[C](val emodb: EmitModuleBuilder, val cb: ClassBuild
       new ((HailClassLoader, FS, HailTaskContext, Region) => C) with java.io.Serializable {
         @transient @volatile private var theClass: Class[_] = null
 
-        def apply(hcl: HailClassLoader, fs: FS, htc: HailTaskContext, region: Region): C = {
+        override def apply(hcl: HailClassLoader, fs: FS, htc: HailTaskContext, region: Region)
+          : C = {
           if (theClass == null) {
             this.synchronized {
               if (theClass == null) {
@@ -953,7 +909,6 @@ final class EmitClassBuilder[C](val emodb: EmitModuleBuilder, val cb: ClassBuild
               }
             }
           }
-          val idx = htc.partitionId()
 
           val f = theClass.getDeclaredConstructor().newInstance().asInstanceOf[C]
           f.asInstanceOf[FunctionWithHailClassLoader].addHailClassLoader(hcl)
@@ -971,7 +926,6 @@ final class EmitClassBuilder[C](val emodb: EmitModuleBuilder, val cb: ClassBuild
             f.asInstanceOf[FunctionWithReferences].addReferenceGenomes(references)
           if (nSerializedAggs != 0)
             f.asInstanceOf[FunctionWithAggRegion].setNumSerialized(nSerializedAggs)
-          f.asInstanceOf[FunctionWithSeededRandomness].setPartitionIndex(idx)
           f
         }
       }
@@ -1261,10 +1215,6 @@ trait FunctionWithLiterals {
   def addAndDecodeLiterals(lit: Array[AnyRef]): Unit
 }
 
-trait FunctionWithSeededRandomness {
-  def setPartitionIndex(idx: Int): Unit
-}
-
 trait FunctionWithBackend {
   def setBackend(spark: BackendUtils): Unit
 }
@@ -1438,7 +1388,7 @@ class EmitMethodBuilder[C](
 trait WrappedEmitMethodBuilder[C] extends WrappedEmitClassBuilder[C] {
   def emb: EmitMethodBuilder[C]
 
-  def ecb: EmitClassBuilder[C] = emb.ecb
+  override def ecb: EmitClassBuilder[C] = emb.ecb
 
   // wrapped MethodBuilder methods
   def mb: MethodBuilder[C] = emb.mb
diff --git a/hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala b/hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala
index c4f170be77a..1fb0a6f31ee 100644
--- a/hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala
+++ b/hail/hail/src/is/hail/expr/ir/EmitCodeBuilder.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.functions.StringFunctions
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SStream, SStreamValue}
@@ -37,10 +38,10 @@ object EmitCodeBuilder {
 }
 
 class EmitCodeBuilder(val emb: EmitMethodBuilder[_], var code: Code[Unit]) extends CodeBuilderLike {
-  def isOpenEnded: Boolean =
+  override def isOpenEnded: Boolean =
     code.isOpenEnded
 
-  def mb: MethodBuilder[_] = emb.mb
+  override def mb: MethodBuilder[_] = emb.mb
 
   override def append(c: Code[Unit]): Unit =
     code = Code(code, c)
@@ -54,7 +55,7 @@ class EmitCodeBuilder(val emb: EmitMethodBuilder[_], var code: Code[Unit]) exten
       L.clear()
     }
 
-  def result(): Code[Unit] = {
+  override def result(): Code[Unit] = {
     val tmp = code
     code = Code._empty
     tmp
diff --git a/hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala b/hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala
index aaea2915e56..36decb86517 100644
--- a/hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala
+++ b/hail/hail/src/is/hail/expr/ir/EmitStreamDistribute.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{const, Code, Value, _}
+import is.hail.asm4s.implicits.valueToRichCodeOutputBuffer
 import is.hail.expr.ir.functions.MathFunctions
 import is.hail.io.{AbstractTypedCodecSpec, OutputBuffer}
 import is.hail.types.physical._
@@ -12,7 +13,6 @@ import is.hail.types.physical.stypes.interfaces.{
 }
 import is.hail.types.physical.stypes.primitives.{SBooleanValue, SInt32, SInt32Value}
 import is.hail.types.virtual.TBaseStruct
-import is.hail.utils._
 
 object EmitStreamDistribute {
 
diff --git a/hail/hail/src/is/hail/expr/ir/Env.scala b/hail/hail/src/is/hail/expr/ir/Env.scala
index d4fd11e8d56..2abf566f083 100644
--- a/hail/hail/src/is/hail/expr/ir/Env.scala
+++ b/hail/hail/src/is/hail/expr/ir/Env.scala
@@ -99,7 +99,7 @@ case class BindingEnv[V](
     newEnv
   }
 
-  def extend(bindings: Bindings[V]): BindingEnv[V] = {
+  override def extend(bindings: Bindings[V]): BindingEnv[V] = {
     val Bindings(all, eval, agg, scan, relational, _) = bindings
     var newEnv = modifyWithoutNewBindings(bindings)
     if (all.nonEmpty) {
@@ -150,9 +150,9 @@ case class BindingEnv[V](
   def allEmpty: Boolean =
     eval.isEmpty && agg.forall(_.isEmpty) && scan.forall(_.isEmpty) && relational.isEmpty
 
-  def promoteAgg: BindingEnv[V] = copy(eval = agg.get, agg = None)
+  override def promoteAgg: BindingEnv[V] = copy(eval = agg.get, agg = None)
 
-  def promoteScan: BindingEnv[V] = copy(eval = scan.get, scan = None)
+  override def promoteScan: BindingEnv[V] = copy(eval = scan.get, scan = None)
 
   def promoteScope(scope: Int): BindingEnv[V] = scope match {
     case Scope.EVAL => this
@@ -160,17 +160,17 @@ case class BindingEnv[V](
     case Scope.SCAN => promoteScan
   }
 
-  def noAgg: BindingEnv[V] = copy(agg = None)
+  override def noAgg: BindingEnv[V] = copy(agg = None)
 
-  def noScan: BindingEnv[V] = copy(scan = None)
+  override def noScan: BindingEnv[V] = copy(scan = None)
 
-  def createAgg: BindingEnv[V] =
+  override def createAgg: BindingEnv[V] =
     copy(agg = Some(eval), scan = scan.map(_ => Env.empty))
 
-  def createScan: BindingEnv[V] =
+  override def createScan: BindingEnv[V] =
     copy(scan = Some(eval), agg = agg.map(_ => Env.empty))
 
-  def onlyRelational(keepAggCapabilities: Boolean = false): BindingEnv[V] =
+  override def onlyRelational(keepAggCapabilities: Boolean = false): BindingEnv[V] =
     BindingEnv(
       agg = if (keepAggCapabilities) agg.map(_ => Env.empty) else None,
       scan = if (keepAggCapabilities) scan.map(_ => Env.empty) else None,
@@ -180,18 +180,18 @@ case class BindingEnv[V](
   def bindEval(name: Name, v: V): BindingEnv[V] =
     copy(eval = eval.bind(name, v))
 
-  def bindEval(bindings: (Name, V)*): BindingEnv[V] =
+  override def bindEval(bindings: (Name, V)*): BindingEnv[V] =
     copy(eval = eval.bindIterable(bindings))
 
   def deleteEval(name: Name): BindingEnv[V] = copy(eval = eval.delete(name))
   def deleteEval(names: IndexedSeq[Name]): BindingEnv[V] = copy(eval = eval.delete(names))
 
-  def noEval: BindingEnv[V] = copy(eval = Env.empty)
+  override def noEval: BindingEnv[V] = copy(eval = Env.empty)
 
   def bindAgg(name: Name, v: V): BindingEnv[V] =
     copy(agg = Some(agg.get.bind(name, v)))
 
-  def bindAgg(bindings: (Name, V)*): BindingEnv[V] =
+  override def bindAgg(bindings: (Name, V)*): BindingEnv[V] =
     copy(agg = Some(agg.get.bindIterable(bindings)))
 
   def aggOrEmpty: Env[V] = agg.getOrElse(Env.empty)
@@ -199,13 +199,13 @@ case class BindingEnv[V](
   def bindScan(name: Name, v: V): BindingEnv[V] =
     copy(scan = Some(scan.get.bind(name, v)))
 
-  def bindScan(bindings: (Name, V)*): BindingEnv[V] =
+  override def bindScan(bindings: (Name, V)*): BindingEnv[V] =
     copy(scan = Some(scan.get.bindIterable(bindings)))
 
   def bindRelational(name: Name, v: V): BindingEnv[V] =
     copy(relational = relational.bind(name, v))
 
-  def bindRelational(bindings: (Name, V)*): BindingEnv[V] =
+  override def bindRelational(bindings: (Name, V)*): BindingEnv[V] =
     copy(relational = relational.bind(bindings: _*))
 
   def scanOrEmpty: Env[V] = scan.getOrElse(Env.empty)
diff --git a/hail/hail/src/is/hail/utils/ExportType.scala b/hail/hail/src/is/hail/expr/ir/ExportType.scala
similarity index 89%
rename from hail/hail/src/is/hail/utils/ExportType.scala
rename to hail/hail/src/is/hail/expr/ir/ExportType.scala
index a2069030bc4..dc603bc0ba7 100644
--- a/hail/hail/src/is/hail/utils/ExportType.scala
+++ b/hail/hail/src/is/hail/expr/ir/ExportType.scala
@@ -1,4 +1,4 @@
-package is.hail.utils
+package is.hail.expr.ir
 
 object ExportType {
   val CONCATENATED = "concatenated"
diff --git a/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala b/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala
index ec4e984577d..56e93430b2b 100644
--- a/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala
+++ b/hail/hail/src/is/hail/expr/ir/ExtractIntervalFilters.scala
@@ -2,6 +2,8 @@ package is.hail.expr.ir
 
 import is.hail.annotations.{ExtendedOrdering, IntervalEndpointOrdering, SafeRow}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.{toRichIndexedSeq, toRichIterable}
 import is.hail.expr.ir.defs._
 import is.hail.rvd.PartitionBoundOrdering
 import is.hail.types.virtual._
@@ -278,11 +280,11 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
     // booleans derived from key comparisons), we don't store top valued fields,
     // and let all missing fields be top implicitly.
     private case class ConcreteStruct(fields: Map[String, Value]) extends StructValue {
-      def apply(field: String): Value = fields.getOrElse(field, top)
+      override def apply(field: String): Value = fields.getOrElse(field, top)
 
-      def values: Iterable[Value] = fields.values
+      override def values: Iterable[Value] = fields.values
 
-      def isKeyPrefix: Boolean = fields.values.view.zipWithIndex.forall {
+      override def isKeyPrefix: Boolean = fields.values.view.zipWithIndex.forall {
         case (f: KeyField, i2) => f.idx == i2
         case _ => false
       }
@@ -505,10 +507,10 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
 
     private case class ConstantStruct(value: Row, t: TStruct)
         extends StructValue with ConstantValue {
-      def apply(field: String): Value = this(t.field(field))
-      def values: Iterable[Value] = t.fields.map(apply)
+      override def apply(field: String): Value = this(t.field(field))
+      override def values: Iterable[Value] = t.fields.map(apply)
       private def apply(field: Field): ConstantValue = ConstantValue(value(field.index), field.typ)
-      def isKeyPrefix: Boolean = false
+      override def isKeyPrefix: Boolean = false
     }
 
     private case class ConstantBool(value: Boolean, keySet: KeySet)
@@ -546,15 +548,15 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
     }
 
     private case class KeyFieldStruct(idx: Int) extends StructValue with KeyField {
-      def apply(field: String): Value = Top
-      def values: Iterable[Value] = Iterable.empty
-      def isKeyPrefix: Boolean = false
+      override def apply(field: String): Value = Top
+      override def values: Iterable[Value] = Iterable.empty
+      override def isKeyPrefix: Boolean = false
     }
 
     private case object Top extends StructValue with BoolValue {
-      def apply(field: String): Value = Top
-      def values: Iterable[Value] = Iterable.empty
-      def isKeyPrefix: Boolean = false
+      override def apply(field: String): Value = Top
+      override def values: Iterable[Value] = Iterable.empty
+      override def isKeyPrefix: Boolean = false
       override def trueBound: KeySet = KeySetLattice.top
       override def falseBound: KeySet = KeySetLattice.top
       override def naBound: KeySet = KeySetLattice.top
@@ -563,9 +565,9 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
     }
 
     private case object Bottom extends StructValue with BoolValue {
-      def apply(field: String): Value = ???
-      def values: Iterable[Value] = ???
-      def isKeyPrefix: Boolean = ???
+      override def apply(field: String): Value = ???
+      override def values: Iterable[Value] = ???
+      override def isKeyPrefix: Boolean = ???
       override def trueBound: KeySet = KeySetLattice.bottom
       override def falseBound: KeySet = KeySetLattice.bottom
       override def naBound: KeySet = KeySetLattice.bottom
@@ -573,10 +575,10 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
       override def isNA: BoolValue = Bottom
     }
 
-    def top: StructValue with BoolValue = Top
-    def bottom: StructValue with BoolValue = Bottom
+    override def top: StructValue with BoolValue = Top
+    override def bottom: StructValue with BoolValue = Bottom
 
-    def join(l: Value, r: Value): Value = (l, r) match {
+    override def join(l: Value, r: Value): Value = (l, r) match {
       case (Bottom, x) => x
       case (x, Bottom) => x
       case (l: ConstantValue, r: ConstantValue) if l.value == r.value => l
@@ -599,7 +601,7 @@ class ExtractIntervalFilters(ctx: ExecuteContext, keyType: TStruct) extends Logg
       case _ => Top
     }
 
-    def meet(l: Value, r: Value): Value = (l, r) match {
+    override def meet(l: Value, r: Value): Value = (l, r) match {
       case (Top, x) => x
       case (x, Top) => x
       case (l: ConstantValue, r: ConstantValue) if l.value == r.value => l
diff --git a/hail/hail/src/is/hail/expr/ir/FoldConstants.scala b/hail/hail/src/is/hail/expr/ir/FoldConstants.scala
index 07ce1f9fbe8..d38da34dfff 100644
--- a/hail/hail/src/is/hail/expr/ir/FoldConstants.scala
+++ b/hail/hail/src/is/hail/expr/ir/FoldConstants.scala
@@ -17,9 +17,9 @@ object FoldConstants {
       {
         case _: Ref |
             _: In |
+            _: LiftMeOut |
             _: RelationalRef |
             _: RelationalLet |
-            _: ApplySeeded |
             _: UUID4 |
             _: ApplyAggOp |
             _: ApplyScanOp |
@@ -37,6 +37,7 @@ object FoldConstants {
             _: NDArrayMatMul |
             _: Trap |
             _: Die |
+            _: RNGSplitStatic |
             _: RNGStateLiteral => None
         case ir: IR if ir.typ.isInstanceOf[TStream] || ir.typ == TVoid => None
         case ir: IR
diff --git a/hail/hail/src/is/hail/expr/ir/ForwardLets.scala b/hail/hail/src/is/hail/expr/ir/ForwardLets.scala
index 50712285c39..46543921c12 100644
--- a/hail/hail/src/is/hail/expr/ir/ForwardLets.scala
+++ b/hail/hail/src/is/hail/expr/ir/ForwardLets.scala
@@ -1,9 +1,9 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.defs.{BaseRef, Binding, Block, In, Ref, Str}
 import is.hail.types.virtual.TVoid
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.Set
 
diff --git a/hail/hail/src/is/hail/expr/ir/FreeVariables.scala b/hail/hail/src/is/hail/expr/ir/FreeVariables.scala
index cf3b01e0f9d..82f57ff4b5a 100644
--- a/hail/hail/src/is/hail/expr/ir/FreeVariables.scala
+++ b/hail/hail/src/is/hail/expr/ir/FreeVariables.scala
@@ -27,7 +27,7 @@ case class FreeVariableBindingEnv(
   aggVars: Option[FreeVariableEnv],
   scanVars: Option[FreeVariableEnv],
 ) extends GenericBindingEnv[FreeVariableBindingEnv, Type] {
-  def extend(bindings: Bindings[Type]): FreeVariableBindingEnv = {
+  override def extend(bindings: Bindings[Type]): FreeVariableBindingEnv = {
     val Bindings(all, eval, agg, scan, relational, dropEval) = bindings
     var newEnv = this
     if (dropEval) newEnv = newEnv.noEval
diff --git a/hail/hail/src/is/hail/expr/ir/GenericLines.scala b/hail/hail/src/is/hail/expr/ir/GenericLines.scala
index c08a1fd4d10..cd16107edd9 100644
--- a/hail/hail/src/is/hail/expr/ir/GenericLines.scala
+++ b/hail/hail/src/is/hail/expr/ir/GenericLines.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.implicits.toRichIterator
 import is.hail.io.compress.BGzipInputStream
 import is.hail.io.fs.{BGZipCompressionCodec, FS, FileStatus, Positioned, PositionedInputStream}
 import is.hail.io.tabix.{TabixLineIterator, TabixReader}
@@ -20,9 +21,9 @@ trait CloseableIterator[T] extends Iterator[T] with AutoCloseable
 
 object CloseableIterator {
   def empty[T]: CloseableIterator[T] = new CloseableIterator[T] {
-    def close(): Unit = ()
-    def hasNext: Boolean = false
-    def next(): T = throw new NoSuchElementException
+    override def close(): Unit = ()
+    override def hasNext: Boolean = false
+    override def next(): T = throw new NoSuchElementException
   }
 }
 
@@ -54,7 +55,7 @@ object GenericLines extends Logging {
             val bgzIS =
               new BGzipInputStream(rawIS, start, end, SplittableCompressionCodec.READ_MODE.BYBLOCK)
             new ProxyInputStream(bgzIS) with Positioned {
-              def getPosition: Long = bgzIS.getVirtualOffset
+              override def getPosition: Long = bgzIS.getVirtualOffset
             }
           } else {
             assert(!split || filePerPartition)
@@ -222,7 +223,7 @@ object GenericLines extends Logging {
 
         private var consumed = false
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (consumed) {
             readLine()
             consumed = false
@@ -230,7 +231,7 @@ object GenericLines extends Logging {
           line != null
         }
 
-        def next(): GenericLine = {
+        override def next(): GenericLine = {
           if (consumed)
             readLine()
           assert(line != null)
@@ -240,7 +241,7 @@ object GenericLines extends Logging {
           line
         }
 
-        def close(): Unit =
+        override def close(): Unit =
           if (!closed) {
             is.close()
             closed = true
@@ -364,8 +365,8 @@ object GenericLines extends Logging {
           private[this] var l = lines.next()
           private[this] var curIdx: Long = lines.getCurIdx()
           private[this] val inner = new Iterator[GenericLine] {
-            def hasNext: Boolean = l != null
-            def next(): GenericLine = {
+            override def hasNext: Boolean = l != null
+            override def next(): GenericLine = {
               assert(l != null)
               val n = l
               val idx = curIdx
@@ -390,9 +391,9 @@ object GenericLines extends Logging {
             start <= pos && pos <= end
           }
 
-          def hasNext: Boolean = inner.hasNext
-          def next(): GenericLine = inner.next()
-          def close(): Unit = lines.close()
+          override def hasNext: Boolean = inner.hasNext
+          override def next(): GenericLine = inner.next()
+          override def close(): Unit = lines.close()
         }
       }
     }
@@ -458,12 +459,12 @@ class GenericLinesRDD(
   body: (Any) => CloseableIterator[GenericLine],
 ) extends RDD[GenericLine](SparkBackend.sparkContext, Seq()) {
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     contexts.iterator.zipWithIndex.map { case (c, i) =>
       new GenericLinesRDDPartition(i, c)
     }.toArray
 
-  def compute(split: Partition, context: TaskContext): Iterator[GenericLine] = {
+  override def compute(split: Partition, context: TaskContext): Iterator[GenericLine] = {
     val it = body(split.asInstanceOf[GenericLinesRDDPartition].context)
     TaskContext.get().addTaskCompletionListener[Unit](_ => it.close()): Unit
     it
diff --git a/hail/hail/src/is/hail/expr/ir/GenericTableValue.scala b/hail/hail/src/is/hail/expr/ir/GenericTableValue.scala
index 7347df780c5..62c07933e43 100644
--- a/hail/hail/src/is/hail/expr/ir/GenericTableValue.scala
+++ b/hail/hail/src/is/hail/expr/ir/GenericTableValue.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.toRichCodeIterator
 import is.hail.backend.ExecuteContext
 import is.hail.expr.ir.LoweredTableReader.LoweredTableReaderCoercer
 import is.hail.expr.ir.defs.{Literal, PartitionReader, ReadPartition, ToStream}
@@ -17,7 +18,6 @@ import is.hail.types.physical.stypes.concrete.{SStackStruct, SStackStructValue}
 import is.hail.types.physical.stypes.interfaces.{primitive, SBaseStructValue, SStreamValue}
 import is.hail.types.physical.stypes.primitives.SInt64
 import is.hail.types.virtual.{TArray, TInt32, TInt64, TStruct, TTuple, TableType, Type}
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 import org.json4s.{Extraction, JValue}
@@ -136,7 +136,7 @@ class PartitionIteratorLongReader(
     }
   }
 
-  def toJValue: JValue =
+  override def toJValue: JValue =
     JObject(
       "category" -> JString("PartitionIteratorLongReader"),
       "fullRowType" -> Extraction.decompose(fullRowType)(PartitionReader.formats),
diff --git a/hail/hail/src/is/hail/expr/ir/IR.scala b/hail/hail/src/is/hail/expr/ir/IR.scala
index 9341d1bb82a..9fb8a621435 100644
--- a/hail/hail/src/is/hail/expr/ir/IR.scala
+++ b/hail/hail/src/is/hail/expr/ir/IR.scala
@@ -63,6 +63,8 @@ trait IR extends BaseIR {
 
 package defs {
 
+  import is.hail.collection.FastSeq
+
   trait TypedIR[T <: Type] extends IR {
     override def typ: T = tcoerce[T](super.typ)
   }
@@ -401,11 +403,11 @@ package defs {
   }
 
   abstract class SimplePartitionWriter extends PartitionWriter {
-    def ctxType: Type = TString
+    override def ctxType: Type = TString
 
-    def returnType: Type = TString
+    override def returnType: Type = TString
 
-    def unionTypeRequiredness(
+    override def unionTypeRequiredness(
       r: TypeWithRequiredness,
       ctxType: TypeWithRequiredness,
       streamType: RIterable,
@@ -425,7 +427,7 @@ package defs {
 
     def postConsume(cb: EmitCodeBuilder, os: Value[OutputStream]): Unit = ()
 
-    final def consumeStream(
+    final override def consumeStream(
       ctx: ExecuteContext,
       cb: EmitCodeBuilder,
       stream: StreamProducer,
@@ -463,8 +465,11 @@ package defs {
   }
 
   final case class SimpleMetadataWriter(val annotationType: Type) extends MetadataWriter {
-    def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
-      : Unit =
+    override def writeMetadata(
+      writeAnnotations: => IEmitCode,
+      cb: EmitCodeBuilder,
+      region: Value[Region],
+    ): Unit =
       writeAnnotations.consume(cb, {}, _ => ())
   }
 
@@ -522,6 +527,8 @@ package defs {
 
   package exts {
 
+    import is.hail.collection.implicits.toRichIterable
+
     abstract class UUID4CompanionExt {
       def apply(): UUID4 = UUID4(genUID())
     }
diff --git a/hail/hail/src/is/hail/expr/ir/IRBuilder.scala b/hail/hail/src/is/hail/expr/ir/IRBuilder.scala
index c40c600ab96..56ac8f59b62 100644
--- a/hail/hail/src/is/hail/expr/ir/IRBuilder.scala
+++ b/hail/hail/src/is/hail/expr/ir/IRBuilder.scala
@@ -1,7 +1,7 @@
 package is.hail.expr.ir
 
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.defs.{Let, Ref, TrivialIR}
-import is.hail.utils.compat.immutable.ArraySeq
 
 object IRBuilder {
   def scoped(f: IRBuilder => IR): IR = {
diff --git a/hail/hail/src/is/hail/expr/ir/InferType.scala b/hail/hail/src/is/hail/expr/ir/InferType.scala
index 83d525969a1..33dd717b839 100644
--- a/hail/hail/src/is/hail/expr/ir/InferType.scala
+++ b/hail/hail/src/is/hail/expr/ir/InferType.scala
@@ -1,10 +1,10 @@
 package is.hail.expr.ir
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs._
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
-import is.hail.utils._
 
 object InferType {
   def apply(ir: IR): Type = {
@@ -114,9 +114,7 @@ object InferType {
       case ToStream(a, _) =>
         val elt = tcoerce[TIterable](a.typ).elementType
         TStream(elt)
-      case RNGStateLiteral() =>
-        TRNGState
-      case RNGSplit(_, _) =>
+      case _: RNGSplit | _: RNGSplitStatic | _: RNGStateLiteral =>
         TRNGState
       case StreamLen(_) => TInt32
       case GroupByKey(collection) =>
diff --git a/hail/hail/src/is/hail/expr/ir/Interpret.scala b/hail/hail/src/is/hail/expr/ir/Interpret.scala
index 3bcf95b4cfa..4829e3d21d8 100644
--- a/hail/hail/src/is/hail/expr/ir/Interpret.scala
+++ b/hail/hail/src/is/hail/expr/ir/Interpret.scala
@@ -4,6 +4,9 @@ import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailTaskContext}
 import is.hail.backend.spark.SparkTaskContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{toRichIterable, toRichIterator}
 import is.hail.expr.ir.analyses.PartitionCounts
 import is.hail.expr.ir.compile.{Compile, CompileWithAggregators}
 import is.hail.expr.ir.defs._
@@ -16,8 +19,8 @@ import is.hail.types.physical.stypes.{PTypeReferenceSingleCodeType, SingleCodeTy
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
+import scala.collection.compat._
 import scala.collection.mutable
 
 import org.apache.spark.sql.Row
@@ -426,7 +429,9 @@ object Interpret extends Logging {
       case GroupByKey(collection) =>
         interpret(collection, env, args).asInstanceOf[IndexedSeq[Row]]
           .groupBy { case Row(k, _) => k }
+          .view
           .mapValues { elt: IndexedSeq[Row] => elt.map { case Row(_, v) => v } }
+          .toMap
       case StreamTake(a, len) =>
         val aValue = interpret(a, env, args)
         val lenValue = interpret(len, env, args)
@@ -780,11 +785,13 @@ object Interpret extends Logging {
         if (struct != null)
           fieldOrder match {
             case Some(fds) =>
-              val newValues = fields.toMap.mapValues(interpret(_, env, args))
+              val m = fields.toMap
               val oldIndices =
                 old.typ.asInstanceOf[TStruct].fields.map(f => f.name -> f.index).toMap
               Row.fromSeq(fds.map(name =>
-                newValues.getOrElse(name, struct.asInstanceOf[Row].get(oldIndices(name)))
+                m.get(name).map(interpret(_, env, args)).getOrElse(
+                  struct.asInstanceOf[Row].get(oldIndices(name))
+                )
               ))
             case None =>
               var t = old.typ.asInstanceOf[TStruct]
@@ -1091,18 +1098,6 @@ object Interpret extends Logging {
         }
 
         wrapped.get(0)
-      case LiftMeOut(child) =>
-        val (Some(PTypeReferenceSingleCodeType(rt)), makeFunction) =
-          Compile[AsmFunction1RegionLong](
-            ctx,
-            FastSeq(),
-            FastSeq(classInfo[Region]),
-            LongInfo,
-            MakeTuple.ordered(FastSeq(child)),
-          )
-        ctx.scopedExecution { (hcl, fs, htc, r) =>
-          SafeRow.read(rt, makeFunction(hcl, fs, htc, r)(r)).asInstanceOf[Row](0)
-        }
       case UUID4(_) =>
         uuid4()
     }
diff --git a/hail/hail/src/is/hail/expr/ir/Interpretable.scala b/hail/hail/src/is/hail/expr/ir/Interpretable.scala
index 4026a7d4fd2..69e5651e543 100644
--- a/hail/hail/src/is/hail/expr/ir/Interpretable.scala
+++ b/hail/hail/src/is/hail/expr/ir/Interpretable.scala
@@ -43,6 +43,8 @@ object Interpretable {
           _: NDArrayWrite |
           _: StreamZipJoinProducers |
           _: ArrayMaximalIndependentSet |
+          _: RNGSplit |
+          _: RNGSplitStatic |
           _: RNGStateLiteral => false
       case Block(bindings, _) =>
         bindings.forall(_.scope == Scope.EVAL)
diff --git a/hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala b/hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala
index c0a5ad09804..31cb0ed95c1 100644
--- a/hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala
+++ b/hail/hail/src/is/hail/expr/ir/LiftRelationalValues.scala
@@ -1,12 +1,12 @@
 package is.hail.expr.ir
 
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.compat.mutable.Growable
 import is.hail.expr.ir.defs.{
   BlockMatrixCollect, BlockMatrixToValueApply, LiftMeOut, RelationalLet, RelationalRef,
   TableAggregate, TableCollect, TableCount, TableGetGlobals, TableToValueApply,
 }
 import is.hail.types.virtual.TVoid
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.compat.mutable.Growable
 
 import scala.collection.mutable
 
diff --git a/hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala
index f1ed169b986..96f1e692922 100644
--- a/hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/LowerMatrixIR.scala
@@ -1,12 +1,14 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.compat.mutable.Growable
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.{WrappedMatrixToTableFunction, WrappedMatrixToValueFunction}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.compat.mutable.Growable
 
 object LowerMatrixIR {
   val entriesFieldName: String = MatrixType.entriesIdentifier
diff --git a/hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala b/hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
index 86ea9a92711..1c2dceb8a31 100644
--- a/hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
+++ b/hail/hail/src/is/hail/expr/ir/LowerOrInterpretNonCompilable.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{Begin, Literal, RelationalLet, RelationalRef}
 import is.hail.expr.ir.lowering.{CanLowerEfficiently, DArrayLowering, LowerToDistributedArrayPass}
 import is.hail.types.virtual.TVoid
diff --git a/hail/hail/src/is/hail/expr/ir/MatrixIR.scala b/hail/hail/src/is/hail/expr/ir/MatrixIR.scala
index 87ec5e0cb7c..04246cc205c 100644
--- a/hail/hail/src/is/hail/expr/ir/MatrixIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/MatrixIR.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.DeprecatedIRBuilder._
 import is.hail.expr.ir.analyses.{ColumnCount, PartitionCounts}
 import is.hail.expr.ir.defs._
@@ -51,7 +52,7 @@ object MatrixIR {
 }
 
 sealed abstract class MatrixIR extends BaseIR {
-  def typ: MatrixType
+  override def typ: MatrixType
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): MatrixIR
 }
@@ -261,7 +262,7 @@ class MatrixNativeReader(
   val params: MatrixNativeReaderParameters,
   spec: AbstractMatrixTableSpec,
 ) extends MatrixReader {
-  def pathsUsed: Seq[String] = FastSeq(params.path)
+  override def pathsUsed: Seq[String] = FastSeq(params.path)
 
   override def renderShort(): String =
     s"(MatrixNativeReader ${params.path} ${params.options.map(_.renderShort()).getOrElse("")})"
@@ -271,13 +272,13 @@ class MatrixNativeReader(
     .sum
     .toInt)
 
-  def partitionCounts: Option[IndexedSeq[Long]] =
+  override def partitionCounts: Option[IndexedSeq[Long]] =
     if (params.options.isEmpty) Some(spec.partitionCounts) else None
 
-  def fullMatrixTypeWithoutUIDs: MatrixType = spec.matrix_type
+  override def fullMatrixTypeWithoutUIDs: MatrixType = spec.matrix_type
 
-  def rowUIDType = TTuple(TInt64, TInt64)
-  def colUIDType = TTuple(TInt64, TInt64)
+  override def rowUIDType = TTuple(TInt64, TInt64)
+  override def colUIDType = TTuple(TInt64, TInt64)
 
   override def lower(
     ctx: ExecuteContext,
@@ -364,7 +365,7 @@ class MatrixNativeReader(
     }
   }
 
-  def toJValue: JValue = {
+  override def toJValue: JValue = {
     implicit val formats: Formats = DefaultFormats
     decomposeWithName(params, "MatrixNativeReader")
   }
@@ -403,12 +404,12 @@ case class MatrixRangeReader(
   val params: MatrixRangeReaderParameters,
   nPartitionsAdj: Int,
 ) extends MatrixReader {
-  def pathsUsed: Seq[String] = FastSeq()
+  override def pathsUsed: Seq[String] = FastSeq()
 
-  def rowUIDType = TInt64
-  def colUIDType = TInt64
+  override def rowUIDType = TInt64
+  override def colUIDType = TInt64
 
-  def fullMatrixTypeWithoutUIDs: MatrixType = MatrixType(
+  override def fullMatrixTypeWithoutUIDs: MatrixType = MatrixType(
     globalType = TStruct.empty,
     colKey = Array("col_idx"),
     colType = TStruct("col_idx" -> TInt32),
@@ -458,7 +459,7 @@ case class MatrixRangeReader(
     ht
   }
 
-  def toJValue: JValue = {
+  override def toJValue: JValue = {
     implicit val formats: Formats = DefaultFormats
     decomposeWithName(params, "MatrixRangeReader")
   }
@@ -529,7 +530,7 @@ case class MatrixFilterCols(child: MatrixIR, pred: IR) extends MatrixIR with Pre
     MatrixFilterCols(newChildren(0).asInstanceOf[MatrixIR], newChildren(1).asInstanceOf[IR])
   }
 
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -544,7 +545,7 @@ case class MatrixFilterRows(child: MatrixIR, pred: IR)
     MatrixFilterRows(newChildren(0).asInstanceOf[MatrixIR], newChildren(1).asInstanceOf[IR])
   }
 
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -558,7 +559,7 @@ case class MatrixChooseCols(child: MatrixIR, oldIndices: IndexedSeq[Int])
     MatrixChooseCols(newChildren(0).asInstanceOf[MatrixIR], oldIndices)
   }
 
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -750,7 +751,7 @@ case class MatrixFilterEntries(child: MatrixIR, pred: IR)
     MatrixFilterEntries(newChildren(0).asInstanceOf[MatrixIR], newChildren(1).asInstanceOf[IR])
   }
 
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -829,7 +830,7 @@ case class MatrixExplodeRows(child: MatrixIR, path: IndexedSeq[String])
 
 case class MatrixRepartition(child: MatrixIR, n: Int, strategy: Int)
     extends MatrixIR with PreservesRows with PreservesCols {
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
 
@@ -846,7 +847,7 @@ case class MatrixRepartition(child: MatrixIR, n: Int, strategy: Int)
 case class MatrixUnionRows(childrenSeq: IndexedSeq[MatrixIR]) extends MatrixIR {
   require(childrenSeq.length > 1)
 
-  def typ: MatrixType = childrenSeq.head.typ
+  override def typ: MatrixType = childrenSeq.head.typ
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): MatrixUnionRows =
     MatrixUnionRows(newChildren.asInstanceOf[IndexedSeq[MatrixIR]])
@@ -854,7 +855,7 @@ case class MatrixUnionRows(childrenSeq: IndexedSeq[MatrixIR]) extends MatrixIR {
 
 case class MatrixDistinctByRow(child: MatrixIR)
     extends MatrixIR with PreservesOrRemovesRows with PreservesCols {
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
 
@@ -869,7 +870,7 @@ case class MatrixDistinctByRow(child: MatrixIR)
 
 case class MatrixRowsHead(child: MatrixIR, n: Long) extends MatrixIR with PreservesCols {
   require(n >= 0)
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = Array(child)
 
@@ -883,7 +884,7 @@ case class MatrixRowsHead(child: MatrixIR, n: Long) extends MatrixIR with Preser
 
 case class MatrixColsHead(child: MatrixIR, n: Int) extends MatrixIR with PreservesRows {
   require(n >= 0)
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = Array(child)
 
@@ -897,7 +898,7 @@ case class MatrixColsHead(child: MatrixIR, n: Int) extends MatrixIR with Preserv
 
 case class MatrixRowsTail(child: MatrixIR, n: Long) extends MatrixIR with PreservesCols {
   require(n >= 0)
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = Array(child)
 
@@ -911,7 +912,7 @@ case class MatrixRowsTail(child: MatrixIR, n: Long) extends MatrixIR with Preser
 
 case class MatrixColsTail(child: MatrixIR, n: Int) extends MatrixIR with PreservesRows {
   require(n >= 0)
-  def typ: MatrixType = child.typ
+  override def typ: MatrixType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = Array(child)
 
@@ -1032,9 +1033,9 @@ case class MatrixFilterIntervals(child: MatrixIR, intervals: IndexedSeq[Interval
 
 case class RelationalLetMatrixTable(name: Name, value: IR, body: MatrixIR)
     extends MatrixIR with PreservesRows {
-  def typ: MatrixType = body.typ
+  override def typ: MatrixType = body.typ
 
-  def childrenSeq: IndexedSeq[BaseIR] = Array(value, body)
+  override def childrenSeq: IndexedSeq[BaseIR] = Array(value, body)
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): MatrixIR = {
     val IndexedSeq(newValue: IR, newBody: MatrixIR) = newChildren
diff --git a/hail/hail/src/is/hail/expr/ir/MatrixValue.scala b/hail/hail/src/is/hail/expr/ir/MatrixValue.scala
index 36c3e164dfd..ccce4ea4ac8 100644
--- a/hail/hail/src/is/hail/expr/ir/MatrixValue.scala
+++ b/hail/hail/src/is/hail/expr/ir/MatrixValue.scala
@@ -2,13 +2,17 @@ package is.hail.expr.ir
 
 import is.hail.annotations._
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
+import is.hail.expr.ir.TableNativeWriter.writeFileReadMe
 import is.hail.io.{BufferSpec, FileWriteMetadata}
 import is.hail.linalg.RowMatrix
 import is.hail.rvd.{AbstractRVDSpec, RVD}
+import is.hail.sparkextras.implicits.toRichRDD
 import is.hail.types.physical.{PArray, PCanonicalStruct, PStruct, PType}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 import is.hail.variant._
 
 import scala.collection.compat._
@@ -107,7 +111,7 @@ case class MatrixValue(
 
     val colsSpec = TableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "../references",
       typ.colsTableType.copy(key = FastSeq[String]()),
       Map(
@@ -144,7 +148,7 @@ case class MatrixValue(
 
     val globalsSpec = TableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "../references",
       TableType(typ.globalType, FastSeq(), TStruct.empty),
       Map(
@@ -175,7 +179,7 @@ case class MatrixValue(
 
     val rowsSpec = TableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "../references",
       typ.rowsTableType,
       Map(
@@ -190,7 +194,7 @@ case class MatrixValue(
 
     val entriesSpec = TableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "../references",
       TableType(entriesRVType, FastSeq(), typ.globalType),
       Map(
@@ -218,7 +222,7 @@ case class MatrixValue(
 
     val spec = MatrixTableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "references",
       typ,
       Map(
@@ -231,7 +235,7 @@ case class MatrixValue(
     )
     spec.write(fs, path)
 
-    writeNativeFileReadMe(fs, path)
+    writeFileReadMe(fs, path)
 
     using(fs.create(path + "/_SUCCESS"))(_ => ())
 
diff --git a/hail/hail/src/is/hail/expr/ir/MatrixWriter.scala b/hail/hail/src/is/hail/expr/ir/MatrixWriter.scala
index cf299fc098a..ae02b779b0a 100644
--- a/hail/hail/src/is/hail/expr/ir/MatrixWriter.scala
+++ b/hail/hail/src/is/hail/expr/ir/MatrixWriter.scala
@@ -2,7 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeOutputBuffer, valueToRichCodeRegion}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.{ByteArrayBuilder, FastSeq}
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.{JSONAnnotationImpex, Nat}
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.lowering.TableStage
@@ -27,7 +30,7 @@ import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives._
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.richUtils.ByteTrackingOutputStream
+import is.hail.utils.implicits.ByteTrackingOutputStream
 import is.hail.variant.{Call, ReferenceGenome}
 
 import java.io.{InputStream, OutputStream}
@@ -61,7 +64,7 @@ case class WrappedMatrixWriter(
   entriesFieldName: String,
   colKey: IndexedSeq[String],
 ) extends TableWriter {
-  def path: String = writer.path
+  override def path: String = writer.path
 
   override def lower(ctx: ExecuteContext, ts: TableStage, r: RTable): IR =
     writer.lower(colsFieldName, entriesFieldName, colKey, ctx, ts, r)
@@ -409,9 +412,9 @@ case class SplitPartitionNativeWriter(
 
   val keyType = spec1.encodedVirtualType.asInstanceOf[TStruct].select(keyFieldNames)._1
 
-  def ctxType: Type = TString
+  override def ctxType: Type = TString
 
-  def returnType: Type = TStruct(
+  override def returnType: Type = TStruct(
     "filePath" -> TString,
     "partitionCounts" -> TInt64,
     "distinctlyKeyed" -> TBoolean,
@@ -419,7 +422,7 @@ case class SplitPartitionNativeWriter(
     "lastKey" -> keyType,
   )
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     r: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -434,7 +437,7 @@ case class SplitPartitionNativeWriter(
     r.union(streamType.required)
   }
 
-  def consumeStream(
+  override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -607,7 +610,7 @@ case class SplitPartitionNativeWriter(
         cb += buff.close()
       }
 
-      stages.flatMap(_.toIterable).zip(filenames).foreach { case (source, destination) =>
+      stages.flatten.zip(filenames).foreach { case (source, destination) =>
         cb += mb.getFS.invoke[String, String, Boolean, Unit](
           "copy",
           source,
@@ -654,7 +657,7 @@ class MatrixSpecHelper(
   def write(fs: FS, nCols: Long, partCounts: Array[Long]): Unit = {
     val spec = MatrixTableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       "references",
       typ,
       Map(
@@ -686,9 +689,9 @@ case class MatrixSpecWriter(
   refRelPath: String,
   log: Boolean,
 ) extends MetadataWriter {
-  def annotationType: Type = TStruct("cols" -> TInt64, "rows" -> TArray(TInt64))
+  override def annotationType: Type = TStruct("cols" -> TInt64, "rows" -> TArray(TInt64))
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -847,9 +850,9 @@ case class VCFPartitionWriter(
 
   val (infoExists, infoIdx) = ExportVCF.lookupVAField(typ.rowType, "info", "INFO", None)
 
-  def returnType: Type = TString
+  override def returnType: Type = TString
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     r: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -858,7 +861,7 @@ case class VCFPartitionWriter(
     r.union(streamType.required)
   }
 
-  final def consumeStream(
+  final override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -1238,7 +1241,8 @@ case class VCFExportFinalizer(
   exportType: String,
   tabix: Boolean,
 ) extends MetadataWriter {
-  def annotationType: Type = TStruct("cols" -> TArray(typ.colType), "partFiles" -> TArray(TString))
+  override def annotationType: Type =
+    TStruct("cols" -> TArray(typ.colType), "partFiles" -> TArray(TString))
 
   private def header(cb: EmitCodeBuilder, annotations: SBaseStructValue): Code[String] = {
     val mb = cb.emb
@@ -1268,8 +1272,11 @@ case class VCFExportFinalizer(
     )
   }
 
-  def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
-    : Unit = {
+  override def writeMetadata(
+    writeAnnotations: => IEmitCode,
+    cb: EmitCodeBuilder,
+    region: Value[Region],
+  ): Unit = {
     val ctx: ExecuteContext = cb.emb.ctx
     val ext = ctx.fs.getCodecExtension(outputPath)
 
@@ -1451,7 +1458,7 @@ case class MatrixGENWriter(
 
 final case class GenVariantWriter(typ: MatrixType, entriesFieldName: String, precision: Int)
     extends SimplePartitionWriter {
-  def consumeElement(
+  override def consumeElement(
     cb: EmitCodeBuilder,
     element: EmitCode,
     os: Value[OutputStream],
@@ -1551,7 +1558,7 @@ final case class GenVariantWriter(typ: MatrixType, entriesFieldName: String, pre
 }
 
 final class GenSampleWriter extends SimplePartitionWriter {
-  def consumeElement(
+  override def consumeElement(
     cb: EmitCodeBuilder,
     element: EmitCode,
     os: Value[OutputStream],
@@ -1675,7 +1682,7 @@ case class BGENPartitionWriter(
   override def returnType: TStruct =
     TStruct("partFile" -> TString, "numVariants" -> TInt64, "dropped" -> TInt64)
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     r: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -1684,7 +1691,7 @@ case class BGENPartitionWriter(
     r.union(streamType.required)
   }
 
-  final def consumeStream(
+  final override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -1962,7 +1969,7 @@ case class BGENPartitionWriter(
 
 case class BGENExportFinalizer(typ: MatrixType, path: String, exportType: String, compression: Int)
     extends MetadataWriter {
-  def annotationType: Type = TStruct(
+  override def annotationType: Type = TStruct(
     "cols" -> TArray(typ.colType),
     "results" -> TArray(TStruct(
       "partFile" -> TString,
@@ -1971,8 +1978,11 @@ case class BGENExportFinalizer(typ: MatrixType, path: String, exportType: String
     )),
   )
 
-  def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
-    : Unit = {
+  override def writeMetadata(
+    writeAnnotations: => IEmitCode,
+    cb: EmitCodeBuilder,
+    region: Value[Region],
+  ): Unit = {
     val annotations = writeAnnotations.getOrAssert(cb).asBaseStruct
     val colValues = annotations.loadField(cb, "cols").getOrAssert(cb).asIndexable
     val sampleIds = cb.memoize(Code.newArray[String](colValues.loadLength))
@@ -2154,14 +2164,14 @@ case class MatrixPLINKWriter(
 
 case class PLINKPartitionWriter(typ: MatrixType, entriesFieldName: String) extends PartitionWriter {
   val ctxType = TStruct("bedFile" -> TString, "bimFile" -> TString)
-  def returnType = TStruct("bedFile" -> TString, "bimFile" -> TString)
+  override def returnType = TStruct("bedFile" -> TString, "bimFile" -> TString)
 
   val locusIdx = typ.rowType.fieldIdx("locus")
   val allelesIdx = typ.rowType.fieldIdx("alleles")
   val varidIdx = typ.rowType.fieldIdx("varid")
   val cmPosIdx = typ.rowType.fieldIdx("cm_position")
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     r: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -2170,7 +2180,7 @@ case class PLINKPartitionWriter(typ: MatrixType, entriesFieldName: String) exten
     r.union(streamType.required)
   }
 
-  final def consumeStream(
+  final override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -2294,10 +2304,13 @@ object PLINKExportFinalizer {
 
 case class PLINKExportFinalizer(typ: MatrixType, path: String, headerPath: String)
     extends MetadataWriter {
-  def annotationType: Type = TArray(TStruct("bedFile" -> TString, "bimFile" -> TString))
+  override def annotationType: Type = TArray(TStruct("bedFile" -> TString, "bimFile" -> TString))
 
-  def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
-    : Unit = {
+  override def writeMetadata(
+    writeAnnotations: => IEmitCode,
+    cb: EmitCodeBuilder,
+    region: Value[Region],
+  ): Unit = {
     val paths = writeAnnotations.getOrAssert(cb).asIndexable
     val bedFiles = cb.memoize(Code.newArray[String](paths.loadLength + 1)) // room for header
     val bimFiles = cb.memoize(Code.newArray[String](paths.loadLength))
diff --git a/hail/hail/src/is/hail/expr/ir/NormalizeNames.scala b/hail/hail/src/is/hail/expr/ir/NormalizeNames.scala
index 738fe308cbd..cdafe9a57d7 100644
--- a/hail/hail/src/is/hail/expr/ir/NormalizeNames.scala
+++ b/hail/hail/src/is/hail/expr/ir/NormalizeNames.scala
@@ -7,7 +7,6 @@ import is.hail.types.virtual.Type
 import is.hail.utils.StackSafe._
 
 import scala.annotation.tailrec
-import scala.collection.mutable
 
 object NormalizeNames {
   def apply[T <: BaseIR](allowFreeVariables: Boolean = false)(ctx: ExecuteContext, ir: T): T =
@@ -99,7 +98,7 @@ class NormalizeNames(freeVariables: Set[Name]) {
       }
       Recur(newName, args, typ).mapChildrenStackSafe(normalizeIR(_, env))
     case ir =>
-      val bindingsMap = mutable.AnyRefMap.empty[Name, Name]
+      val bindingsMap = is.hail.collection.compat.mutable.AnyRefMap.empty[Name, Name]
       val updateEnv: (BindingEnv[Name], Bindings[Type]) => BindingEnv[Name] =
         if (needsRenaming(ir)) { (env, bindings) =>
           val bindingsNames = bindings.map((name, _) => bindingsMap.getOrElseUpdate(name, gen()))
diff --git a/hail/hail/src/is/hail/expr/ir/Param.scala b/hail/hail/src/is/hail/expr/ir/Param.scala
index f9935540e52..70f87b47300 100644
--- a/hail/hail/src/is/hail/expr/ir/Param.scala
+++ b/hail/hail/src/is/hail/expr/ir/Param.scala
@@ -1,22 +1,22 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s.{BooleanInfo, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.types.physical.stypes.{EmitType, SType, SValue, SingleCodeType}
 import is.hail.types.virtual.Type
-import is.hail.utils.FastSeq
 
 sealed trait ParamType {
   def nCodes: Int
 }
 
 case class CodeParamType(ti: TypeInfo[_]) extends ParamType {
-  def nCodes: Int = 1
+  override def nCodes: Int = 1
 
   override def toString: String = s"CodeParam($ti)"
 }
 
 case class SCodeParamType(st: SType) extends ParamType {
-  def nCodes: Int = st.nSettables
+  override def nCodes: Int = st.nSettables
 
   override def toString: String = s"SCodeParam($st, $nCodes)"
 }
@@ -34,25 +34,25 @@ trait EmitParamType extends ParamType {
       ts :+ BooleanInfo
   }
 
-  final def nCodes: Int = valueTupleTypes.length
+  final override def nCodes: Int = valueTupleTypes.length
 
   protected def definedValueTupleTypes(): IndexedSeq[TypeInfo[_]]
 }
 
 case class SingleCodeEmitParamType(required: Boolean, sct: SingleCodeType) extends EmitParamType {
-  def virtualType: Type = sct.virtualType
+  override def virtualType: Type = sct.virtualType
 
-  def definedValueTupleTypes(): IndexedSeq[TypeInfo[_]] = FastSeq(sct.ti)
+  override def definedValueTupleTypes(): IndexedSeq[TypeInfo[_]] = FastSeq(sct.ti)
 
   override def toString: String = s"SingleCodeEmitParamType($required, $sct)"
 }
 
 case class SCodeEmitParamType(et: EmitType) extends EmitParamType {
-  def required: Boolean = et.required
+  override def required: Boolean = et.required
 
-  def virtualType: Type = et.st.virtualType
+  override def virtualType: Type = et.st.virtualType
 
-  def definedValueTupleTypes(): IndexedSeq[TypeInfo[_]] = et.st.settableTupleTypes()
+  override def definedValueTupleTypes(): IndexedSeq[TypeInfo[_]] = et.st.settableTupleTypes()
 }
 
 sealed trait Param
diff --git a/hail/hail/src/is/hail/expr/ir/Parser.scala b/hail/hail/src/is/hail/expr/ir/Parser.scala
index 57b71de9300..45d9720d7ff 100644
--- a/hail/hail/src/is/hail/expr/ir/Parser.scala
+++ b/hail/hail/src/is/hail/expr/ir/Parser.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.{JSONAnnotationImpex, Nat, ParserUtils}
 import is.hail.expr.ir.agg._
 import is.hail.expr.ir.defs._
@@ -35,23 +36,23 @@ abstract class Token extends Positional {
 }
 
 final case class IdentifierToken(value: String) extends Token {
-  def getName: String = "identifier"
+  override def getName: String = "identifier"
 }
 
 final case class StringToken(value: String) extends Token {
-  def getName: String = "string"
+  override def getName: String = "string"
 }
 
 final case class IntegerToken(value: Long) extends Token {
-  def getName: String = "integer"
+  override def getName: String = "integer"
 }
 
 final case class FloatToken(value: Double) extends Token {
-  def getName: String = "float"
+  override def getName: String = "float"
 }
 
 final case class PunctuationToken(value: String) extends Token {
-  def getName: String = "punctuation"
+  override def getName: String = "punctuation"
 }
 
 object IRLexer extends JavaTokenParsers {
@@ -66,7 +67,7 @@ object IRLexer extends JavaTokenParsers {
 
   def quotedLiteral(delim: Char, what: String): Parser[String] =
     new Parser[String] {
-      def apply(in: Input): ParseResult[String] = {
+      override def apply(in: Input): ParseResult[String] = {
         var r = in
 
         val source = in.source
@@ -538,12 +539,6 @@ object IRParser {
         punctuation(it, "}")
         val fields = args.zipWithIndex.map { case ((id, t), i) => Field(id, t, i) }
         TStruct(fields)
-      case "Union" =>
-        punctuation(it, "{")
-        val args = repsepUntil(it, type_field, PunctuationToken(","), PunctuationToken("}"))
-        punctuation(it, "}")
-        val cases = args.zipWithIndex.map { case ((id, t), i) => Case(id, t, i) }
-        TUnion(cases)
       case "Void" => TVoid
     }
     typ
@@ -939,6 +934,9 @@ object IRParser {
           state <- ir_value_expr(ctx)(it)
           dynBitstring <- ir_value_expr(ctx)(it)
         } yield RNGSplit(state, dynBitstring)
+      case "RNGSplitStatic" =>
+        val staticUid = int64_literal(it)
+        ir_value_expr(ctx)(it) map { RNGSplitStatic(_, staticUid) }
       case "ArrayLen" => ir_value_expr(ctx)(it).map(ArrayLen)
       case "StreamLen" => ir_value_expr(ctx)(it).map(StreamLen)
       case "StreamIota" =>
@@ -1075,6 +1073,16 @@ object IRParser {
           elem <- ir_value_expr(ctx)(it)
         } yield LowerBoundOnOrderedCollection(col, elem, onKey)
       case "GroupByKey" => ir_value_expr(ctx)(it).map(GroupByKey)
+      case "StreamBufferedAggregate" =>
+        val n = name(it)
+        val aggSigs = p_agg_sigs(ctx)(it)
+        val size = int32_literal(it)
+        for {
+          stream <- ir_value_expr(ctx)(it)
+          init <- ir_value_expr(ctx)(it)
+          key <- ir_value_expr(ctx)(it)
+          seq <- ir_value_expr(ctx)(it)
+        } yield StreamBufferedAggregate(stream, init, key, seq, n, aggSigs, size)
       case "StreamMap" =>
         val n = name(it)
         for {
@@ -1370,14 +1378,6 @@ object IRParser {
           msg <- ir_value_expr(ctx)(it)
           result <- ir_value_expr(ctx)(it)
         } yield ConsoleLog(msg, result)
-      case "ApplySeeded" =>
-        val function = identifier(it)
-        val staticUID = int64_literal(it)
-        val rt = type_expr(it)
-        for {
-          rngState <- ir_value_expr(ctx)(it)
-          args <- ir_value_children(ctx)(it)
-        } yield ApplySeeded(function, args, rngState, staticUID, rt)
       case "ApplyIR" =>
         apply_like(ctx, ApplyIR.apply)(it)
       case "ApplySpecial" =>
@@ -2108,7 +2108,7 @@ object IRParser {
   }
 
   def parse[T](s: String, f: (TokenIterator) => T): T = {
-    val it = IRLexer.parse(s).toIterator.buffered
+    val it = IRLexer.parse(s).iterator.buffered
     f(it)
   }
 
@@ -2151,8 +2151,6 @@ object IRParser {
 
   def parseStructType(code: String): TStruct = tcoerce[TStruct](parse(code, type_expr))
 
-  def parseUnionType(code: String): TUnion = tcoerce[TUnion](parse(code, type_expr))
-
   def parseRVDType(code: String): RVDType = parse(code, rvd_type_expr)
 
   def parseTableType(code: String): TableType = parse(code, table_type_expr)
diff --git a/hail/hail/src/is/hail/expr/ir/Pretty.scala b/hail/hail/src/is/hail/expr/ir/Pretty.scala
index 84ea2570ace..84a42200654 100644
--- a/hail/hail/src/is/hail/expr/ir/Pretty.scala
+++ b/hail/hail/src/is/hail/expr/ir/Pretty.scala
@@ -1,6 +1,9 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{toRichIterable, RichIterable}
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir.Pretty.prettyBooleanLiteral
 import is.hail.expr.ir.agg._
@@ -8,9 +11,7 @@ import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.RelationalFunctions
 import is.hail.types.virtual.{MatrixType, TArray, TInterval, TStream, TableType, Type}
 import is.hail.utils.{space => _, _}
-import is.hail.utils.compat.immutable.ArraySeq
 import is.hail.utils.prettyPrint._
-import is.hail.utils.richUtils.RichIterable
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -124,10 +125,13 @@ class Pretty(
   def prettyIntOpt(x: Option[Int]): String =
     x.map(_.toString).getOrElse("None")
 
+  def prettyLong(x: Long): Doc =
+    text(x.toString)
+
   def prettyLongs(x: IndexedSeq[Long], elideLiterals: Boolean): Doc = {
     val truncate = elideLiterals && x.length > MAX_VALUES_TO_LOG
-    val view = if (truncate) x.view else x.view(0, MAX_VALUES_TO_LOG)
-    val docs = view.map(i => text(i.toString))
+    val view = if (truncate) x.view else x.view.slice(0, MAX_VALUES_TO_LOG)
+    val docs = view.map(prettyLong)
     concat(docs.intersperse[Doc](
       "(",
       softline,
@@ -135,10 +139,13 @@ class Pretty(
     ))
   }
 
+  def prettyInt(x: Int): Doc =
+    text(x.toString)
+
   def prettyInts(x: IndexedSeq[Int], elideLiterals: Boolean): Doc = {
     val truncate = elideLiterals && x.length > MAX_VALUES_TO_LOG
-    val view = if (truncate) x.view else x.view(0, MAX_VALUES_TO_LOG)
-    val docs = view.map(i => text(i.toString))
+    val view = if (truncate) x.view else x.view.slice(0, MAX_VALUES_TO_LOG)
+    val docs = view.map(prettyInt)
     concat(docs.intersperse[Doc](
       "(",
       softline,
@@ -268,6 +275,7 @@ class Pretty(
       else
         FastSeq(prettyName(name), t.parsableString())
     case RelationalLet(name, _, _) if !elideBindings => single(prettyName(name))
+    case RNGSplitStatic(_, staticUid) => single(prettyLong(staticUid))
     case ApplyBinaryPrimOp(op, _, _) => single(Pretty.prettyClass(op))
     case ApplyUnaryPrimOp(op, _) => single(Pretty.prettyClass(op))
     case ApplyComparisonOp(op, _, _) => single(op.render())
@@ -277,6 +285,8 @@ class Pretty(
     case MakeArray(_, typ) => single(typ.parsableString())
     case MakeStream(_, typ, requiresMemoryManagementPerElement) =>
       FastSeq(typ.parsableString(), Pretty.prettyBooleanLiteral(requiresMemoryManagementPerElement))
+    case StreamBufferedAggregate(_, _, _, _, name, sigs, size) =>
+      ArraySeq(prettyName(name), prettyPhysicalAggSigs(sigs), prettyInt(size))
     case StreamIota(_, _, requiresMemoryManagementPerElement) =>
       FastSeq(Pretty.prettyBooleanLiteral(requiresMemoryManagementPerElement))
     case StreamRange(_, _, _, requiresMemoryManagementPerElement, errorID) =>
@@ -422,8 +432,6 @@ class Pretty(
       )
     case Apply(function, typeArgs, _, t, errorID) =>
       FastSeq(s"$errorID", prettyIdentifier(function), prettyTypes(typeArgs), t.parsableString())
-    case ApplySeeded(function, _, _, staticUID, t) =>
-      FastSeq(prettyIdentifier(function), staticUID.toString, t.parsableString())
     case ApplySpecial(function, typeArgs, _, t, errorID) =>
       FastSeq(s"$errorID", prettyIdentifier(function), prettyTypes(typeArgs), t.parsableString())
     case SelectFields(_, fields) =>
@@ -439,26 +447,26 @@ class Pretty(
         Pretty.prettyBooleanLiteral(dropCols),
         Pretty.prettyBooleanLiteral(dropRows),
         if (elideLiterals) reader.renderShort()
-        else '"' + StringEscapeUtils.escapeString(JsonMethods.compact(reader.toJValue)) + '"',
+        else s""""${StringEscapeUtils.escapeString(JsonMethods.compact(reader.toJValue))}"""",
       )
     case MatrixWrite(_, writer) =>
-      single('"' + StringEscapeUtils.escapeString(
-        Serialization.write(writer)(MatrixWriter.formats)
-      ) + '"')
+      single(
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(MatrixWriter.formats))}""""
+      )
     case MatrixMultiWrite(_, writer) =>
-      single('"' + StringEscapeUtils.escapeString(
-        Serialization.write(writer)(MatrixNativeMultiWriter.formats)
-      ) + '"')
+      single(
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(MatrixNativeMultiWriter.formats))}""""
+      )
     case BlockMatrixRead(reader) =>
-      single('"' + StringEscapeUtils.escapeString(JsonMethods.compact(reader.toJValue)) + '"')
+      single(s""""${StringEscapeUtils.escapeString(JsonMethods.compact(reader.toJValue))}"""")
     case BlockMatrixWrite(_, writer) =>
-      single('"' + StringEscapeUtils.escapeString(
-        Serialization.write(writer)(BlockMatrixWriter.formats)
-      ) + '"')
+      single(
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(BlockMatrixWriter.formats))}""""
+      )
     case BlockMatrixMultiWrite(_, writer) =>
-      single('"' + StringEscapeUtils.escapeString(
-        Serialization.write(writer)(BlockMatrixWriter.formats)
-      ) + '"')
+      single(
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(BlockMatrixWriter.formats))}""""
+      )
     case BlockMatrixBroadcast(_, inIndexExpr, shape, blockSize) =>
       FastSeq(
         prettyInts(inIndexExpr, elideLiterals),
@@ -515,16 +523,16 @@ class Pretty(
         if (typ == tr.fullType) "None" else typ.parsableString(),
         Pretty.prettyBooleanLiteral(dropRows),
         if (elideLiterals) tr.renderShort()
-        else '"' + StringEscapeUtils.escapeString(JsonMethods.compact(tr.toJValue)) + '"',
+        else s""""${StringEscapeUtils.escapeString(JsonMethods.compact(tr.toJValue))}"""",
       )
     case TableWrite(_, writer) =>
       single(
-        '"' + StringEscapeUtils.escapeString(Serialization.write(writer)(TableWriter.formats)) + '"'
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(TableWriter.formats))}""""
       )
     case TableMultiWrite(_, writer) =>
-      single('"' + StringEscapeUtils.escapeString(
-        Serialization.write(writer)(WrappedMatrixNativeMultiWriter.formats)
-      ) + '"')
+      single(
+        s""""${StringEscapeUtils.escapeString(Serialization.write(writer)(WrappedMatrixNativeMultiWriter.formats))}""""
+      )
     case TableKeyBy(_, keys, isSorted) =>
       FastSeq(prettyIdentifiers(keys), Pretty.prettyBooleanLiteral(isSorted))
     case TableRange(n, nPartitions) => FastSeq(n.toString, nPartitions.toString)
@@ -681,169 +689,192 @@ class Pretty(
 
   def ssaStyle(ir: BaseIR): String = {
     def childIsStrict(ir: BaseIR, i: Int): Boolean = blockArgs(ir, i).isEmpty
+    def some(as: (Name, String)*) = Some(as.toFastSeq)
 
-    def blockArgs(ir: BaseIR, i: Int): Option[IndexedSeq[(Name, String)]] = ir match {
-      case If(_, _, _) =>
-        if (i > 0) Some(FastSeq()) else None
-      case _: Switch =>
-        if (i > 0) Some(FastSeq()) else None
-      case TailLoop(name, args, _, _) => if (i == args.length)
-          Some(args.map { case (name, _) => name -> "loopvar" } :+
-            name -> "loop")
-        else None
-      case StreamMap(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamZip(as, names, _, _, _) =>
-        if (i == as.length) Some(names.map(_ -> "elt")) else None
-      case StreamZipJoin(as, _, curKey, curVals, _) =>
-        if (i == as.length)
-          Some(Array(curKey -> "key", curVals -> "elts"))
-        else
-          None
-      case StreamFor(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamFlatMap(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamFilter(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamTakeWhile(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamDropWhile(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamFold(_, _, accumName, valueName, _) =>
-        if (i == 2) Some(Array(accumName -> "accum", valueName -> "elt")) else None
-      case StreamFold2(_, accum, valueName, _, _) =>
-        if (i <= accum.length)
-          None
-        else if (i < 2 * accum.length + 1)
-          Some(Array(valueName -> "elt") ++ accum.map { case (name, _) => name -> "accum" })
-        else
-          Some(accum.map { case (name, _) => name -> "accum" })
-      case RunAggScan(_, name, _, _, _, _) =>
-        if (i == 2 || i == 3) Some(Array(name -> "elt")) else None
-      case StreamScan(_, _, accumName, valueName, _) =>
-        if (i == 2) Some(Array(accumName -> "accum", valueName -> "elt")) else None
-      case StreamAggScan(_, name, _) =>
-        if (i == 1) Some(FastSeq(name -> "elt")) else None
-      case StreamJoinRightDistinct(_, _, _, _, l, r, _, _) =>
-        if (i == 2) Some(Array(l -> "l_elt", r -> "r_elt")) else None
-      case StreamLeftIntervalJoin(_, _, _, _, l, r, _) =>
-        if (i == 2) Some(Array(l -> "l_elt", r -> "r_elts")) else None
-      case ArraySort(_, left, right, _) =>
-        if (i == 1) Some(Array(left -> "l", right -> "r")) else None
-      case AggArrayPerElement(_, elementName, indexName, _, _, _) =>
-        if (i == 1) Some(Array(elementName -> "elt", indexName -> "idx")) else None
-      case AggFold(_, _, _, accumName, otherAccumName, _) =>
-        if (i == 1) Some(Array(accumName -> "accum"))
-        else if (i == 2) Some(Array(accumName -> "l", otherAccumName -> "r"))
-        else None
-      case NDArrayMap(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case NDArrayMap2(_, _, lName, rName, _, _) => if (i == 2)
-          Some(Array(lName -> "l_elt", rName -> "r_elt"))
-        else
-          None
-      case CollectDistributedArray(_, _, cname, gname, _, _, _, _) =>
-        if (i == 2) Some(Array(cname -> "ctx", gname -> "g")) else None
-      case TableAggregate(_, _) =>
-        if (i == 1) Some(Array(TableIR.globalName -> "g", TableIR.rowName -> "row")) else None
-      case MatrixAggregate(_, _) =>
-        if (i == 1) Some(Array(
-          MatrixIR.globalName -> "g",
-          MatrixIR.colName -> "col",
-          MatrixIR.rowName -> "row",
-          MatrixIR.entryName -> "entry",
-        ))
-        else None
-      case TableFilter(_, _) =>
-        if (i == 1) Some(Array(TableIR.globalName -> "g", TableIR.rowName -> "row")) else None
-      case TableMapGlobals(_, _) =>
-        if (i == 1) Some(Array(TableIR.globalName -> "g")) else None
-      case TableMapRows(_, _) =>
-        if (i == 1) Some(Array(TableIR.globalName -> "g", TableIR.rowName -> "row")) else None
-      case TableAggregateByKey(_, _) =>
-        if (i == 1) Some(Array(TableIR.globalName -> "g", TableIR.rowName -> "row")) else None
-      case TableKeyByAndAggregate(_, _, _, _, _) =>
-        if (i == 1 || i == 2)
-          Some(Array(TableIR.globalName -> "g", TableIR.rowName -> "row"))
-        else None
-      case TableMapPartitions(_, g, p, _, _, _) =>
-        if (i == 1) Some(Array(g -> "g", p -> "part")) else None
-      case MatrixMapRows(_, _) =>
-        if (i == 1) Some(Array(
-          MatrixIR.globalName -> "g",
-          MatrixIR.rowName -> "row",
-          MatrixIR.colName -> "col",
-          MatrixIR.entryName -> "entry",
-          Name("n_cols") -> "n_cols",
-        ))
-        else None
-      case MatrixFilterRows(_, _) =>
-        if (i == 1) Some(Array(MatrixIR.globalName -> "g", MatrixIR.rowName -> "row")) else None
-      case MatrixMapCols(_, _, _) =>
-        if (i == 1) Some(Array(
-          MatrixIR.globalName -> "g",
-          MatrixIR.rowName -> "row",
-          MatrixIR.colName -> "col",
-          MatrixIR.entryName -> "entry",
-          Name("n_rows") -> "n_rows",
-        ))
-        else None
-      case MatrixFilterCols(_, _) =>
-        if (i == 1) Some(Array(MatrixIR.globalName -> "g", MatrixIR.colName -> "col")) else None
-      case MatrixMapEntries(_, _) =>
-        if (i == 1) Some(Array(
-          MatrixIR.globalName -> "g",
-          MatrixIR.colName -> "col",
-          MatrixIR.rowName -> "row",
-          MatrixIR.entryName -> "entry",
-        ))
-        else None
-      case MatrixFilterEntries(_, _) =>
-        if (i == 1) Some(Array(
-          MatrixIR.globalName -> "g",
-          MatrixIR.colName -> "col",
-          MatrixIR.rowName -> "row",
-          MatrixIR.entryName -> "entry",
-        ))
-        else None
-      case MatrixMapGlobals(_, _) =>
-        if (i == 1) Some(Array(MatrixIR.globalName -> "g")) else None
-      case MatrixAggregateColsByKey(_, _, _) =>
-        if (i == 1)
-          Some(Array(
-            MatrixIR.globalName -> "g",
-            MatrixIR.rowName -> "row",
-            MatrixIR.colName -> "col",
-            MatrixIR.entryName -> "entry",
-          ))
-        else if (i == 2)
-          Some(Array(MatrixIR.globalName -> "g", MatrixIR.colName -> "col"))
-        else
-          None
-      case MatrixAggregateRowsByKey(_, _, _) =>
-        if (i == 1)
-          Some(Array(
-            MatrixIR.globalName -> "g",
-            MatrixIR.rowName -> "row",
-            MatrixIR.colName -> "col",
-            MatrixIR.entryName -> "entry",
-          ))
-        else if (i == 2)
-          Some(Array(MatrixIR.globalName -> "g", MatrixIR.rowName -> "row"))
-        else
+    lazy val matrixBlockArgs =
+      some(
+        MatrixIR.globalName -> "g",
+        MatrixIR.colName -> "col",
+        MatrixIR.rowName -> "row",
+        MatrixIR.entryName -> "entry",
+      )
+
+    lazy val tableBlockArgs =
+      some(
+        TableIR.globalName -> "g",
+        TableIR.rowName -> "row",
+      )
+
+    def blockArgs(ir: BaseIR, i: Int): Option[IndexedSeq[(Name, String)]] =
+      ir match {
+        case AggArrayPerElement(_, elementName, indexName, _, _, _) =>
+          if (i == 1) some(elementName -> "elt", indexName -> "idx")
+          else None
+        case AggExplode(_, name, _, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case _: AggFilter =>
+          if (i == 1) some()
+          else None
+        case AggFold(_, _, _, accumName, otherAccumName, _) =>
+          if (i == 1) some(accumName -> "accum")
+          else if (i == 2) some(accumName -> "l", otherAccumName -> "r")
+          else None
+        case _: AggGroupBy =>
+          if (i == 1) some()
+          else None
+        case ArraySort(_, left, right, _) =>
+          if (i == 1) some(left -> "l", right -> "r")
+          else None
+        case BlockMatrixMap(_, eltName, _, _) =>
+          if (i == 1) some(eltName -> "elt")
+          else None
+        case BlockMatrixMap2(_, _, lName, rName, _, _) =>
+          if (i == 2) some(lName -> "l", rName -> "r")
+          else None
+        case _: Coalesce =>
+          some()
+        case CollectDistributedArray(_, _, cname, gname, _, _, _, _) =>
+          if (i == 2) some(cname -> "ctx", gname -> "g")
+          else None
+        case _: ConsoleLog =>
+          if (i == 1) some()
+          else None
+        case _: If =>
+          if (i > 0) some()
+          else None
+        case _: LiftMeOut =>
+          some()
+        case _: MatrixAggregate =>
+          if (i == 1) matrixBlockArgs
+          else None
+        case _: MatrixAggregateColsByKey =>
+          if (i == 1) matrixBlockArgs
+          else if (i == 2) some(MatrixIR.globalName -> "g", MatrixIR.colName -> "col")
+          else None
+        case _: MatrixAggregateRowsByKey =>
+          if (i == 1) matrixBlockArgs
+          else if (i == 2) some(MatrixIR.globalName -> "g", MatrixIR.rowName -> "row")
+          else None
+        case _: MatrixFilterCols =>
+          if (i == 1) some(MatrixIR.globalName -> "g", MatrixIR.colName -> "col")
+          else None
+        case _: MatrixFilterEntries =>
+          if (i == 1) matrixBlockArgs
+          else None
+        case _: MatrixFilterRows =>
+          if (i == 1) some(MatrixIR.globalName -> "g", MatrixIR.rowName -> "row")
+          else None
+        case _: MatrixMapCols =>
+          if (i == 1) matrixBlockArgs map { _ :+ (Name("n_rows") -> "n_rows") }
+          else None
+        case _: MatrixMapEntries =>
+          if (i == 1) matrixBlockArgs
+          else None
+        case _: MatrixMapGlobals =>
+          if (i == 1) some(MatrixIR.globalName -> "g")
+          else None
+        case _: MatrixMapRows =>
+          if (i == 1) matrixBlockArgs map { _ :+ (Name("n_rows") -> "n_rows") }
+          else None
+        case NDArrayMap(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case NDArrayMap2(_, _, lName, rName, _, _) =>
+          if (i == 2) some(lName -> "l_elt", rName -> "r_elt")
+          else None
+        case RunAggScan(_, name, _, _, _, _) =>
+          if (i == 2 || i == 3) some(name -> "elt")
+          else None
+        case StreamAgg(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamAggScan(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case s: StreamBufferedAggregate =>
+          if (i >= 2) some(s.name -> "elt")
+          else None
+        case StreamDropWhile(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamFlatMap(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamFilter(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamFold(_, _, accumName, valueName, _) =>
+          if (i == 2) some(accumName -> "accum", valueName -> "elt")
+          else None
+        case StreamFold2(_, accum, valueName, _, _) =>
+          if (i <= accum.length) None
+          else if (i < 2 * accum.length + 1) Some((valueName -> "elt") +: accum.map {
+            case (name, _) => name -> "accum"
+          })
+          else Some(accum.map { case (name, _) => name -> "accum" })
+        case StreamFor(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamJoinRightDistinct(_, _, _, _, l, r, _, _) =>
+          if (i == 2) some(l -> "l_elt", r -> "r_elt")
+          else None
+        case StreamLeftIntervalJoin(_, _, _, _, l, r, _) =>
+          if (i == 2) some(l -> "l_elt", r -> "r_elts")
+          else None
+        case StreamMap(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamScan(_, _, accumName, valueName, _) =>
+          if (i == 2) some(accumName -> "accum", valueName -> "elt")
+          else None
+        case StreamTakeWhile(_, name, _) =>
+          if (i == 1) some(name -> "elt")
+          else None
+        case StreamZip(as, names, _, _, _) =>
+          if (i == as.length) Some(names.map(_ -> "elt"))
+          else None
+        case StreamZipJoin(as, _, curKey, curVals, _) =>
+          if (i == as.length) some(curKey -> "key", curVals -> "elts")
+          else None
+        case StreamZipJoinProducers(_, cname, _, _, k, v, _) =>
+          if (i == 1) some(cname -> "elt")
+          else if (i == 2) some(k -> "key", v -> "val")
+          else None
+        case _: Switch =>
+          if (i > 0) some()
+          else None
+        case _: TableAggregate =>
+          if (i == 1) tableBlockArgs
+          else None
+        case _: TableAggregateByKey =>
+          if (i == 1) tableBlockArgs
+          else None
+        case _: TableFilter =>
+          if (i == 1) tableBlockArgs
+          else None
+        case _: TableKeyByAndAggregate =>
+          if (i == 1 || i == 2) tableBlockArgs
+          else None
+        case _: TableMapGlobals =>
+          if (i == 1) some(TableIR.globalName -> "g")
+          else None
+        case TableMapPartitions(_, g, p, _, _, _) =>
+          if (i == 1) some(g -> "g", p -> "part")
+          else None
+        case _: TableMapRows =>
+          if (i == 1) tableBlockArgs
+          else None
+        case TailLoop(name, args, _, _) =>
+          if (i == args.length) Some(args.map { case (name, _) =>
+            name -> "loopvar"
+          } :+ name -> "loop")
+          else None
+        case _: Trap =>
+          some()
+        case _ =>
           None
-      case BlockMatrixMap(_, eltName, _, _) =>
-        if (i == 1) Some(Array(eltName -> "elt")) else None
-      case BlockMatrixMap2(_, _, lName, rName, _, _) =>
-        if (i == 2) Some(Array(lName -> "l", rName -> "r")) else None
-      case AggExplode(_, name, _, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case StreamAgg(_, name, _) =>
-        if (i == 1) Some(Array(name -> "elt")) else None
-      case _ =>
-        None
-    }
+      }
 
     var identCounter: Int = 0
     val idents = collection.mutable.Map.empty[String, Int]
diff --git a/hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala b/hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala
index 7bad42e7218..e9d97327da9 100644
--- a/hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala
+++ b/hail/hail/src/is/hail/expr/ir/PruneDeadFields.scala
@@ -2,13 +2,14 @@ package is.hail.expr.ir
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs._
 import is.hail.types._
 import is.hail.types.virtual._
 import is.hail.types.virtual.TIterable.elementType
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -1385,7 +1386,7 @@ object PruneDeadFields extends Logging {
         recurMax(ir, 0)
 
       case Block(bindings, _) =>
-        val typeStates = mutable.AnyRefMap.empty[Name, TypeState]
+        val typeStates = is.hail.collection.compat.mutable.AnyRefMap.empty[Name, TypeState]
         recurWithTypeStates(ir, bindings.length, requestedType, typeStates)
         for (i <- bindings.indices.reverse)
           recurWithTypeStates(ir, i, typeStates(bindings(i).name).newType, typeStates)
@@ -1497,7 +1498,7 @@ object PruneDeadFields extends Logging {
 
       case StreamFold2(_, accum, valueName, seq, _) =>
         recur(ir, 2 * accum.length + 1, requestedType)
-        val seqBindings = mutable.AnyRefMap.empty[Name, TypeState]
+        val seqBindings = is.hail.collection.compat.mutable.AnyRefMap.empty[Name, TypeState]
         seq.indices.foreach(i => recurMaxWithTypeStates(ir, accum.length + 1 + i, seqBindings))
         accum.indices.foreach(i => recurMax(ir, i + 1))
         recur(ir, 0, TStream(seqBindings(valueName).newType))
@@ -1607,7 +1608,7 @@ object PruneDeadFields extends Logging {
         recur(ir, 1, requestedType)
 
       case RunAggScan(_, name, _, _, _, _) =>
-        val bindings = mutable.AnyRefMap.empty[Name, TypeState]
+        val bindings = is.hail.collection.compat.mutable.AnyRefMap.empty[Name, TypeState]
 
         recurWithTypeStates(ir, 3, TIterable.elementType(requestedType), bindings)
         recurMaxWithTypeStates(ir, 2, bindings)
diff --git a/hail/hail/src/is/hail/expr/ir/Random.scala b/hail/hail/src/is/hail/expr/ir/Random.scala
index 86150a95eea..f1e82757301 100644
--- a/hail/hail/src/is/hail/expr/ir/Random.scala
+++ b/hail/hail/src/is/hail/expr/ir/Random.scala
@@ -1,7 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s._
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import net.sourceforge.jdistlib.{Beta, Gamma, HyperGeometric, Poisson}
 import net.sourceforge.jdistlib.rng.RandomEngine
diff --git a/hail/hail/src/is/hail/expr/ir/Requiredness.scala b/hail/hail/src/is/hail/expr/ir/Requiredness.scala
index 13b4e5b1831..bdffa159bc6 100644
--- a/hail/hail/src/is/hail/expr/ir/Requiredness.scala
+++ b/hail/hail/src/is/hail/expr/ir/Requiredness.scala
@@ -1,6 +1,9 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.GetElement
 import is.hail.methods.ForceCountTable
@@ -9,7 +12,6 @@ import is.hail.types.physical.PType
 import is.hail.types.physical.stypes.{EmitType, PTypeReferenceSingleCodeType, StreamSingleCodeType}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -554,7 +556,7 @@ class Requiredness(val usesAndDefs: UsesAndDefs, ctx: ExecuteContext) {
         requiredness.union(node.children.forall { case c: IR => lookup(c).required })
 
       // always required
-      case _: I32 | _: I64 | _: F32 | _: F64 | _: Str | True() | False() | _: IsNA | _: Die | _: UUID4 | _: RNGStateLiteral | _: RNGSplit =>
+      case _: I32 | _: I64 | _: F32 | _: F64 | _: Str | True() | False() | _: IsNA | _: Die | _: UUID4 | _: RNGSplit | _: RNGSplitStatic | _: RNGStateLiteral =>
       case _: CombOpValue | _: AggStateValue =>
       case Trap(child) =>
         // error message field is missing if the child runs without error
@@ -805,9 +807,9 @@ class Requiredness(val usesAndDefs: UsesAndDefs, ctx: ExecuteContext) {
         lookup(old) match {
           case oldReq: RStruct =>
             requiredness.union(oldReq.required)
-            val fieldMap = fields.toMap.mapValues(lookup)
+            val fieldMap = fields.toMap
             tcoerce[RStruct](requiredness).fields.foreach { f =>
-              f.typ.unionFrom(fieldMap.getOrElse(f.name, oldReq.field(f.name)))
+              f.typ.unionFrom(fieldMap.get(f.name).map(lookup).getOrElse(oldReq.field(f.name)))
             }
           case _ => fields.foreach { case (n, f) =>
               tcoerce[RStruct](requiredness).field(n).unionFrom(lookup(f))
diff --git a/hail/hail/src/is/hail/expr/ir/Simplify.scala b/hail/hail/src/is/hail/expr/ir/Simplify.scala
index 2d4ef2e3ced..ea31e4804e2 100644
--- a/hail/hail/src/is/hail/expr/ir/Simplify.scala
+++ b/hail/hail/src/is/hail/expr/ir/Simplify.scala
@@ -1,6 +1,9 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{toRichIndexedSeq, toRichIterable, toRichMap}
 import is.hail.expr.ir.analyses.{ColumnCount, PartitionCounts, PartitionCountsOrColumnCount}
 import is.hail.expr.ir.defs._
 import is.hail.io.bgen.MatrixBGENReader
@@ -8,7 +11,6 @@ import is.hail.rvd.PartitionBoundOrdering
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 
@@ -64,7 +66,6 @@ object Simplify {
   private[this] def hasMissingStrictChild(x: IR): Boolean = {
     x match {
       case _: Apply |
-          _: ApplySeeded |
           _: ApplyUnaryPrimOp |
           _: ApplyBinaryPrimOp |
           _: ArrayRef |
diff --git a/hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala b/hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala
index 55b3f7f7d8a..b65e58b7065 100644
--- a/hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala
+++ b/hail/hail/src/is/hail/expr/ir/SpecializedArrayBuilders.scala
@@ -4,8 +4,6 @@ import is.hail.annotations.Region
 import is.hail.asm4s._
 import is.hail.types.physical.stypes.SingleCodeType
 
-import scala.reflect.ClassTag
-
 class StagedArrayBuilder(
   cb: EmitCodeBuilder,
   val elt: SingleCodeType,
@@ -150,7 +148,7 @@ final class IntMissingArrayBuilder(initialCapacity: Int)
     b(i)
   }
 
-  def ensureCapacity(n: Int): Unit = {
+  override def ensureCapacity(n: Int): Unit = {
     if (b.length < n) {
       val newCapacity = math.max(n, b.length * 2)
       val newb = new Array[Int](newCapacity)
@@ -210,7 +208,7 @@ final class LongMissingArrayBuilder(initialCapacity: Int)
     b(i)
   }
 
-  def ensureCapacity(n: Int): Unit = {
+  override def ensureCapacity(n: Int): Unit = {
     if (b.length < n) {
       val newCapacity = math.max(n, b.length * 2)
       val newb = new Array[Long](newCapacity)
@@ -270,7 +268,7 @@ final class FloatMissingArrayBuilder(initialCapacity: Int)
     b(i)
   }
 
-  def ensureCapacity(n: Int): Unit = {
+  override def ensureCapacity(n: Int): Unit = {
     if (b.length < n) {
       val newCapacity = math.max(n, b.length * 2)
       val newb = new Array[Float](newCapacity)
@@ -330,7 +328,7 @@ final class DoubleMissingArrayBuilder(initialCapacity: Int)
     b(i)
   }
 
-  def ensureCapacity(n: Int): Unit = {
+  override def ensureCapacity(n: Int): Unit = {
     if (b.length < n) {
       val newCapacity = math.max(n, b.length * 2)
       val newb = new Array[Double](newCapacity)
@@ -390,7 +388,7 @@ final class BooleanMissingArrayBuilder(initialCapacity: Int)
     b(i)
   }
 
-  def ensureCapacity(n: Int): Unit = {
+  override def ensureCapacity(n: Int): Unit = {
     if (b.length < n) {
       val newCapacity = math.max(n, b.length * 2)
       val newb = new Array[Boolean](newCapacity)
@@ -440,558 +438,3 @@ final class BooleanMissingArrayBuilder(initialCapacity: Int)
     }
   }
 }
-
-final class ByteArrayArrayBuilder(initialCapacity: Int) {
-
-  var size_ : Int = 0
-  private var b: Array[Array[Byte]] = new Array[Array[Byte]](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): Array[Byte] = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[Array[Byte]](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def add(x: Array[Byte]): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Array[Byte]): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Array[Byte]] = b.slice(0, size_)
-}
-
-final class LongArrayBuilder(initialCapacity: Int = 16) {
-
-  var size_ : Int = 0
-  var b: Array[Long] = new Array[Long](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): Long = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, (b.length * 2))
-      val newb = new Array[Long](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def +=(x: Long): Unit = add(x)
-
-  def ++=(xs: Array[Long]) = {
-    val newLen = size + xs.length
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, xs.length)
-    size_ = newLen
-  }
-
-  def ++=(xs: Array[Long], n: Int) = {
-    val newLen = size + n
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, n)
-    size_ = newLen
-  }
-
-  def add(x: Long): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Long): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Long] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[Long](initialCapacity)
-  }
-
-  def appendFrom(ab2: LongArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): Long = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class IntArrayBuilder(initialCapacity: Int = 16) {
-
-  var size_ : Int = 0
-  var b: Array[Int] = new Array[Int](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): Int = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[Int](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def setSizeUninitialized(n: Int) = {
-    ensureCapacity(n)
-    size_ = n
-  }
-
-  def +=(x: Int): Unit = add(x)
-
-  def ++=(xs: Array[Int]) = {
-    val newLen = size + xs.length
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, xs.length)
-    size_ = newLen
-  }
-
-  def ++=(xs: Array[Int], n: Int) = {
-    val newLen = size + n
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, n)
-    size_ = newLen
-  }
-
-  def add(x: Int): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Int): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Int] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[Int](initialCapacity)
-  }
-
-  def appendFrom(ab2: IntArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): Int = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class DoubleArrayBuilder(initialCapacity: Int = 16) {
-
-  var size_ : Int = 0
-  var b: Array[Double] = new Array[Double](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): Double = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[Double](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def setSizeUninitialized(n: Int) = {
-    ensureCapacity(n)
-    size_ = n
-  }
-
-  def +=(x: Double): Unit = add(x)
-
-  def ++=(xs: Array[Double]) = {
-    val newLen = size + xs.length
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, xs.length)
-    size_ = newLen
-  }
-
-  def ++=(xs: Array[Double], n: Int) = {
-    val newLen = size + n
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, n)
-    size_ = newLen
-  }
-
-  def add(x: Double): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Double): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Double] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[Double](initialCapacity)
-  }
-
-  def appendFrom(ab2: DoubleArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): Double = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class ByteArrayBuilder(initialCapacity: Int = 16) {
-
-  var size_ : Int = 0
-  var b: Array[Byte] = new Array[Byte](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def setSizeUnchecked(n: Int): Unit =
-    size_ = n
-
-  def apply(i: Int): Byte = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[Byte](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def +=(x: Byte) = add(x)
-
-  def ++=(xs: Array[Byte]) = {
-    val newLen = size + xs.length
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, xs.length)
-    size_ = newLen
-  }
-
-  def ++=(xs: Array[Byte], n: Int) = {
-    val newLen = size + n
-    ensureCapacity(newLen)
-    System.arraycopy(xs, 0, b, size_, n)
-    size_ = newLen
-  }
-
-  def add(x: Byte): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Byte): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Byte] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[Byte](initialCapacity)
-  }
-
-  def appendFrom(ab2: ByteArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): Byte = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class BooleanArrayBuilder(initialCapacity: Int = 16) {
-
-  var size_ : Int = 0
-  var b: Array[Boolean] = new Array[Boolean](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): Boolean = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[Boolean](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def +=(x: Boolean) = add(x)
-
-  def add(x: Boolean): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: Boolean): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[Boolean] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[Boolean](initialCapacity)
-  }
-
-  def appendFrom(ab2: BooleanArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): Boolean = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class StringArrayBuilder(initialCapacity: Int = 16) {
-  var size_ : Int = 0
-  var b: Array[String] = new Array[String](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): String = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[String](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def +=(x: String) = add(x)
-
-  def add(x: String): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def update(i: Int, x: String): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[String] = {
-    val a = new Array[String](size_)
-    System.arraycopy(b, 0, a, 0, size_)
-    a
-  }
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[String](initialCapacity)
-  }
-
-  def appendFrom(ab2: StringArrayBuilder): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): String = {
-    size_ -= 1
-    b(size)
-  }
-}
-
-final class AnyRefArrayBuilder[T <: AnyRef](initialCapacity: Int = 16)(implicit ct: ClassTag[T]) {
-
-  var size_ : Int = 0
-  var b: Array[T] = new Array[T](initialCapacity)
-
-  def size: Int = size_
-
-  def setSize(n: Int): Unit = {
-    require(n >= 0 && n <= size)
-    size_ = n
-  }
-
-  def apply(i: Int): T = {
-    require(i >= 0 && i < size)
-    b(i)
-  }
-
-  def ensureCapacity(n: Int): Unit = {
-    if (b.length < n) {
-      val newCapacity = math.max(n, b.length * 2)
-      val newb = new Array[T](newCapacity)
-      Array.copy(b, 0, newb, 0, size_)
-      b = newb
-    }
-  }
-
-  def add(x: T): Unit = {
-    ensureCapacity(size_ + 1)
-    b(size_) = x
-    size_ += 1
-  }
-
-  def +=(x: T): Unit = add(x)
-
-  def update(i: Int, x: T): Unit = {
-    require(i >= 0 && i < size)
-    b(i) = x
-  }
-
-  def clear(): Unit = size_ = 0
-
-  def result(): Array[T] = b.slice(0, size_)
-
-  def clearAndResize(): Unit = {
-    size_ = 0
-    if (b.length > initialCapacity)
-      b = new Array[T](initialCapacity)
-  }
-
-  def appendFrom(ab2: AnyRefArrayBuilder[T]): Unit = {
-    ensureCapacity(size_ + ab2.size_)
-    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
-    size_ = size_ + ab2.size_
-  }
-
-  def pop(): T = {
-    size_ -= 1
-    b(size)
-  }
-
-  def clearAndSetNull(): Unit = {
-    clear()
-    var i = 0
-    while (i < b.length) {
-      b(i) = (null.asInstanceOf[T])
-      i += 1
-    }
-  }
-
-  def setSizeUninitialized(size: Int): Unit = {
-    ensureCapacity(size)
-    size_ = size
-  }
-}
diff --git a/hail/hail/src/is/hail/expr/ir/StringTableReader.scala b/hail/hail/src/is/hail/expr/ir/StringTableReader.scala
index 65239f25d69..4e32d1a9082 100644
--- a/hail/hail/src/is/hail/expr/ir/StringTableReader.scala
+++ b/hail/hail/src/is/hail/expr/ir/StringTableReader.scala
@@ -3,10 +3,12 @@ package is.hail.expr.ir
 import is.hail.annotations.Region
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{Literal, MakeStruct, PartitionReader, ReadPartition, Ref, ToStream}
 import is.hail.expr.ir.functions.StringFunctions
 import is.hail.expr.ir.lowering.{LowererUnsupportedOperation, TableStage, TableStageDependency}
 import is.hail.expr.ir.streams.StreamProducer
+import is.hail.io.checkGzipOfGlobbedFiles
 import is.hail.io.fs.{FS, FileListEntry}
 import is.hail.rvd.RVDPartitioner
 import is.hail.types.{BaseTypeWithRequiredness, RStruct, VirtualTypeWithReq}
@@ -16,7 +18,6 @@ import is.hail.types.physical.stypes.concrete.{SJavaString, SStackStruct, SStack
 import is.hail.types.physical.stypes.interfaces.{SBaseStructValue, SStreamValue}
 import is.hail.types.physical.stypes.primitives.{SInt64, SInt64Value}
 import is.hail.types.virtual._
-import is.hail.utils.{checkGzipOfGlobbedFiles, FastSeq}
 
 import org.json4s.{Extraction, Formats, JValue}
 
diff --git a/hail/hail/src/is/hail/expr/ir/Sym.scala b/hail/hail/src/is/hail/expr/ir/Sym.scala
deleted file mode 100644
index 863093d9d84..00000000000
--- a/hail/hail/src/is/hail/expr/ir/Sym.scala
+++ /dev/null
@@ -1,56 +0,0 @@
-package is.hail.expr.ir
-
-import is.hail.utils.StringEscapeUtils
-
-// FIXME Sym instead of Symbol so we don't conflict with Scala's Symbol which is currently used by by the IR DSL
-object Sym {
-  var counter: Int = 0
-
-  def gen(base: String): Sym = {
-    counter += 1
-    Generated("j", base, counter)
-  }
-}
-
-abstract class Sym
-
-case class Identifier(name: String) extends Sym {
-  override def toString: String =
-    if (name.matches("""\p{javaJavaIdentifierStart}\p{javaJavaIdentifierPart}*"""))
-      name
-    else
-      s"`${StringEscapeUtils.escapeString(name, backticked = true)}`"
-}
-
-// lang is one of "py" or "j"
-case class Generated(lang: String, base: String, i: Int) extends Sym {
-  override def toString: String = s":$lang$base-$i"
-}
-
-case object GlobalSym {
-  override def toString: String = ":global"
-}
-
-case object ColSym {
-  override def toString: String = ":col"
-}
-
-case object RowSym {
-  override def toString: String = ":row"
-}
-
-case object EntrySym extends Sym {
-  override def toString: String = ":entry"
-}
-
-case object ColsSym extends Sym {
-  override def toString: String = ":cols"
-}
-
-case object GlobalAndColsSym extends Sym {
-  override def toString: String = ":global-and-cols"
-}
-
-case object EntriesSym extends Sym {
-  override def toString: String = ":entries"
-}
diff --git a/hail/hail/src/is/hail/expr/ir/TableIR.scala b/hail/hail/src/is/hail/expr/ir/TableIR.scala
index 736a32563e3..0431529db83 100644
--- a/hail/hail/src/is/hail/expr/ir/TableIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/TableIR.scala
@@ -2,7 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeInputBuffer
 import is.hail.backend.{ExecuteContext, HailStateManager, HailTaskContext, TaskFinalizer}
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.{
@@ -50,7 +53,7 @@ object TableIR {
 }
 
 sealed abstract class TableIR extends BaseIR {
-  def typ: TableType
+  override def typ: TableType
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableIR
 }
@@ -157,11 +160,10 @@ object LoweredTableReader extends Logging {
           keyRef.name,
           MakeStruct(FastSeq(
             "key" -> keyRef,
-            "token" -> invokeSeeded(
+            "token" -> invoke(
               "rand_unif",
-              1,
               TFloat64,
-              RNGStateLiteral(),
+              RNGSplitStatic(RNGStateLiteral(), 1L),
               F64(0.0),
               F64(1.0),
             ),
@@ -612,7 +614,7 @@ case class PartitionRVDReader(rvd: RVD, uidFieldName: String) extends PartitionR
     tr
   }
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -736,12 +738,12 @@ case class PartitionRVDReader(rvd: RVD, uidFieldName: String) extends PartitionR
     }
   }
 
-  def toJValue: JValue =
+  override def toJValue: JValue =
     JString("<PartitionRVDReader>") // cannot be parsed, but need a printout for Pretty
 }
 
 trait AbstractNativeReader extends PartitionReader {
-  def uidFieldName: String
+  override def uidFieldName: String
 
   def spec: AbstractTypedCodecSpec
 
@@ -758,16 +760,16 @@ trait AbstractNativeReader extends PartitionReader {
     tr
   }
 
-  def fullRowType: TStruct = spec.encodedVirtualType.asInstanceOf[TStruct]
+  override def fullRowType: TStruct = spec.encodedVirtualType.asInstanceOf[TStruct]
     .insertFields(Array(uidFieldName -> TTuple(TInt64, TInt64)))
 }
 
 case class PartitionNativeReader(spec: AbstractTypedCodecSpec, uidFieldName: String)
     extends AbstractNativeReader {
 
-  def contextType: Type = TStruct("partitionIndex" -> TInt64, "partitionPath" -> TString)
+  override def contextType: Type = TStruct("partitionIndex" -> TInt64, "partitionPath" -> TString)
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -857,7 +859,7 @@ case class PartitionNativeReader(spec: AbstractTypedCodecSpec, uidFieldName: Str
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
 
 case class PartitionNativeIntervalReader(
@@ -876,9 +878,9 @@ case class PartitionNativeIntervalReader(
   lazy val contextType: Type = RVDPartitioner.intervalIRRepresentation(partitioner.kType)
   require(partitioner.kType.size > 0)
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -941,6 +943,7 @@ case class PartitionNativeIntervalReader(
       val currIdxInPartition = mb.genFieldThisRef[Long]("n_to_read")
       val stopIdxInPartition = mb.genFieldThisRef[Long]("n_to_read")
       val finalizer = mb.genFieldThisRef[TaskFinalizer]("finalizer")
+      cb.assign(finalizer, cb.emb.ecb.getTaskContext.invoke[TaskFinalizer]("newFinalizer"))
 
       val startPartitionIndex = mb.genFieldThisRef[Int]("start_part")
       val currPartitionIdx = mb.genFieldThisRef[Int]("curr_part")
@@ -996,8 +999,6 @@ case class PartitionNativeIntervalReader(
           cb.assign(streamFirst, true)
           cb.assign(currIdxInPartition, 0L)
           cb.assign(stopIdxInPartition, 0L)
-
-          cb.assign(finalizer, cb.emb.ecb.getTaskContext.invoke[TaskFinalizer]("newFinalizer"))
         }
 
         override val elementRegion: Settable[Region] = region
@@ -1177,7 +1178,7 @@ case class PartitionNativeReaderIndexed(
   key: IndexedSeq[String],
   uidFieldName: String,
 ) extends AbstractNativeReader {
-  def contextType: Type = TStruct(
+  override def contextType: Type = TStruct(
     "partitionIndex" -> TInt64,
     "partitionPath" -> TString,
     "indexPath" -> TString,
@@ -1186,7 +1187,7 @@ case class PartitionNativeReaderIndexed(
     ),
   )
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -1315,7 +1316,7 @@ case class PartitionNativeReaderIndexed(
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
 
 // Result uses the uid field name and values from the right input, and ignores
@@ -1323,9 +1324,9 @@ case class PartitionNativeReaderIndexed(
 case class PartitionZippedNativeReader(left: PartitionReader, right: PartitionReader)
     extends PartitionReader {
 
-  def uidFieldName = right.uidFieldName
+  override def uidFieldName = right.uidFieldName
 
-  def contextType: Type = TStruct(
+  override def contextType: Type = TStruct(
     "leftContext" -> left.contextType,
     "rightContext" -> right.contextType,
   )
@@ -1356,7 +1357,7 @@ case class PartitionZippedNativeReader(left: PartitionReader, right: PartitionRe
     TStruct.concat(leftStruct, rightStruct)
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 
   override def emitStream(
     ctx: ExecuteContext,
@@ -1460,12 +1461,15 @@ case class PartitionZippedNativeIntervalReader(
 
   private lazy val zippedReader = PartitionZippedNativeReader(rowsReader, entriesReader)
 
-  def contextType = rowsReader.contextType
-  def fullRowType = zippedReader.fullRowType
-  def rowRequiredness(requestedType: TStruct): RStruct = zippedReader.rowRequiredness(requestedType)
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def contextType = rowsReader.contextType
+  override def fullRowType = zippedReader.fullRowType
+
+  override def rowRequiredness(requestedType: TStruct): RStruct =
+    zippedReader.rowRequiredness(requestedType)
+
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -1491,7 +1495,7 @@ case class PartitionZippedIndexedNativeReader(
   uidFieldName: String,
 ) extends PartitionReader {
 
-  def contextType: Type = {
+  override def contextType: Type = {
     TStruct(
       "partitionIndex" -> TInt64,
       "leftPartitionPath" -> TString,
@@ -1518,7 +1522,7 @@ case class PartitionZippedIndexedNativeReader(
     (leftStruct, rightStruct)
   }
 
-  def rowRequiredness(requestedType: TStruct): RStruct = {
+  override def rowRequiredness(requestedType: TStruct): RStruct = {
     val (leftStruct, rightStruct) = splitRequestedTypes(requestedType)
     val rt = TypeWithRequiredness(requestedType).asInstanceOf[RStruct]
     val pt = specLeft.decodedPType(leftStruct).asInstanceOf[PStruct].insertFields(
@@ -1538,13 +1542,13 @@ case class PartitionZippedIndexedNativeReader(
     ),
   )
 
-  def fullRowType: TStruct =
+  override def fullRowType: TStruct =
     (specLeft.encodedVirtualType.asInstanceOf[TStruct] ++ specRight.encodedVirtualType.asInstanceOf[
       TStruct
     ])
       .insertFields(Array(uidFieldName -> TTuple(TInt64, TInt64, TInt64, TInt64)))
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -1697,7 +1701,7 @@ case class PartitionZippedIndexedNativeReader(
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
 
 case class TableNativeReaderParameters(
@@ -1709,25 +1713,25 @@ class TableNativeReader(
   val params: TableNativeReaderParameters,
   val spec: AbstractTableSpec,
 ) extends TableReaderWithExtraUID {
-  def pathsUsed: Seq[String] = Array(params.path)
+  override def pathsUsed: Seq[String] = Array(params.path)
 
   val filterIntervals: Boolean = params.options.map(_.filterIntervals).getOrElse(false)
 
-  def partitionCounts: Option[IndexedSeq[Long]] =
+  override def partitionCounts: Option[IndexedSeq[Long]] =
     if (params.options.isDefined) None else Some(spec.partitionCounts)
 
   override def isDistinctlyKeyed: Boolean = spec.isDistinctlyKeyed
 
-  def uidType = TTuple(TInt64, TInt64)
+  override def uidType = TTuple(TInt64, TInt64)
 
-  def fullTypeWithoutUIDs = spec.table_type
+  override def fullTypeWithoutUIDs = spec.table_type
 
   override def concreteRowRequiredness(ctx: ExecuteContext, requestedType: TableType)
     : VirtualTypeWithReq =
     VirtualTypeWithReq(tcoerce[PStruct](spec.rowsComponent.rvdSpec(ctx.fs, params.path)
       .typedCodecSpec.encodedType.decodedPType(requestedType.rowType)))
 
-  protected def uidRequiredness: VirtualTypeWithReq =
+  override protected def uidRequiredness: VirtualTypeWithReq =
     VirtualTypeWithReq(PCanonicalTuple(true, PInt64Required, PInt64Required))
 
   override def globalRequiredness(ctx: ExecuteContext, requestedType: TableType)
@@ -1813,7 +1817,7 @@ case class TableNativeZippedReader(
   specLeft: AbstractTableSpec,
   specRight: AbstractTableSpec,
 ) extends TableReaderWithExtraUID {
-  def pathsUsed: Seq[String] = FastSeq(pathLeft, pathRight)
+  override def pathsUsed: Seq[String] = FastSeq(pathLeft, pathRight)
 
   override def renderShort(): String =
     s"(TableNativeZippedReader $pathLeft $pathRight ${options.map(_.renderShort()).getOrElse("")})"
@@ -1830,7 +1834,7 @@ case class TableNativeZippedReader(
   require(specLeft.partitionCounts sameElements specRight.partitionCounts)
   require(specLeft.version == specRight.version)
 
-  def partitionCounts: Option[IndexedSeq[Long]] =
+  override def partitionCounts: Option[IndexedSeq[Long]] =
     if (intervals.isEmpty) Some(specLeft.partitionCounts) else None
 
   override def uidType = TTuple(TInt64, TInt64)
@@ -1974,7 +1978,7 @@ case class TableFromBlockMatrixNativeReader(
   params: TableFromBlockMatrixNativeReaderParameters,
   metadata: BlockMatrixMetadata,
 ) extends TableReaderWithExtraUID {
-  def pathsUsed: Seq[String] = FastSeq(params.path)
+  override def pathsUsed: Seq[String] = FastSeq(params.path)
 
   val partitionRanges = (0 until params.nPartitions).map { i =>
     val nRows = metadata.nRows
@@ -2040,7 +2044,7 @@ case class TableFromBlockMatrixNativeReader(
   override def toJValue: JValue =
     decomposeWithName(params, "TableFromBlockMatrixNativeReader")(TableReader.formats)
 
-  def renderShort(): String = defaultRender()
+  override def renderShort(): String = defaultRender()
 }
 
 object TableRead {
@@ -2192,7 +2196,7 @@ case class TableRange(n: Int, nPartitions: Int) extends TableIR {
 case class TableFilter(child: TableIR, pred: IR) extends TableIR with PreservesOrRemovesRows {
   val childrenSeq: IndexedSeq[BaseIR] = Array(child, pred)
 
-  def typ: TableType = child.typ
+  override def typ: TableType = child.typ
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableFilter = {
     assert(newChildren.length == 2)
@@ -2205,7 +2209,7 @@ case class TableFilter(child: TableIR, pred: IR) extends TableIR with PreservesO
 case class TableHead(child: TableIR, n: Long) extends TableIR {
   require(n >= 0, fatal(s"TableHead: n must be non-negative! Found '$n'."))
   lazy val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
-  def typ: TableType = child.typ
+  override def typ: TableType = child.typ
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableHead = {
     val IndexedSeq(newChild: TableIR) = newChildren
@@ -2216,7 +2220,7 @@ case class TableHead(child: TableIR, n: Long) extends TableIR {
 case class TableTail(child: TableIR, n: Long) extends TableIR {
   require(n >= 0, fatal(s"TableTail: n must be non-negative! Found '$n'."))
   lazy val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
-  def typ: TableType = child.typ
+  override def typ: TableType = child.typ
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableTail = {
     val IndexedSeq(newChild: TableIR) = newChildren
@@ -2232,7 +2236,7 @@ object RepartitionStrategy {
 
 case class TableRepartition(child: TableIR, n: Int, strategy: Int)
     extends TableIR with PreservesRows {
-  def typ: TableType = child.typ
+  override def typ: TableType = child.typ
 
   lazy val childrenSeq: IndexedSeq[BaseIR] = FastSeq(child)
 
@@ -2466,7 +2470,7 @@ case class TableUnion(childrenSeq: IndexedSeq[TableIR]) extends TableIR {
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableUnion =
     TableUnion(newChildren.map(_.asInstanceOf[TableIR]))
 
-  def typ: TableType = childrenSeq(0).typ
+  override def typ: TableType = childrenSeq(0).typ
 }
 
 case class MatrixRowsTable(child: MatrixIR) extends TableIR with PreservesRows {
@@ -2477,7 +2481,7 @@ case class MatrixRowsTable(child: MatrixIR) extends TableIR with PreservesRows {
     MatrixRowsTable(newChildren(0).asInstanceOf[MatrixIR])
   }
 
-  def typ: TableType = child.typ.rowsTableType
+  override def typ: TableType = child.typ.rowsTableType
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -2490,7 +2494,7 @@ case class MatrixColsTable(child: MatrixIR) extends TableIR {
     MatrixColsTable(newChildren(0).asInstanceOf[MatrixIR])
   }
 
-  def typ: TableType = child.typ.colsTableType
+  override def typ: TableType = child.typ.colsTableType
 }
 
 case class MatrixEntriesTable(child: MatrixIR) extends TableIR {
@@ -2502,7 +2506,7 @@ case class MatrixEntriesTable(child: MatrixIR) extends TableIR {
     MatrixEntriesTable(newChildren(0).asInstanceOf[MatrixIR])
   }
 
-  def typ: TableType = child.typ.entriesTableType
+  override def typ: TableType = child.typ.entriesTableType
 }
 
 case class TableDistinct(child: TableIR) extends TableIR with PreservesOrRemovesRows {
@@ -2513,7 +2517,7 @@ case class TableDistinct(child: TableIR) extends TableIR with PreservesOrRemoves
     TableDistinct(newChild.asInstanceOf[TableIR])
   }
 
-  def typ: TableType = child.typ
+  override def typ: TableType = child.typ
 
   override def preservesRowsOrColsFrom: BaseIR = child
 }
@@ -2715,14 +2719,14 @@ case class BlockMatrixToTable(child: BlockMatrixIR) extends TableIR {
 
 case class RelationalLetTable(name: Name, value: IR, body: TableIR)
     extends TableIR with PreservesRows {
-  def typ: TableType = body.typ
+  override def typ: TableType = body.typ
 
-  def childrenSeq: IndexedSeq[BaseIR] = Array(value, body)
+  override def childrenSeq: IndexedSeq[BaseIR] = Array(value, body)
 
   override protected def copyWithNewChildren(newChildren: IndexedSeq[BaseIR]): TableIR = {
     val IndexedSeq(newValue: IR, newBody: TableIR) = newChildren
     RelationalLetTable(name, newValue, newBody)
   }
 
-  def preservesRowsOrColsFrom: BaseIR = body
+  override def preservesRowsOrColsFrom: BaseIR = body
 }
diff --git a/hail/hail/src/is/hail/expr/ir/TableValue.scala b/hail/hail/src/is/hail/expr/ir/TableValue.scala
index e2ec7d70069..97832de1df5 100644
--- a/hail/hail/src/is/hail/expr/ir/TableValue.scala
+++ b/hail/hail/src/is/hail/expr/ir/TableValue.scala
@@ -4,6 +4,9 @@ import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
 import is.hail.backend.spark.{SparkBackend, SparkTaskContext}
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.TableAnnotationImpex
 import is.hail.expr.ir.agg.IndependentExtractedAggs
 import is.hail.expr.ir.compile.{Compile, CompileWithAggregators}
@@ -12,6 +15,7 @@ import is.hail.expr.ir.lowering.{RVDToTableStage, TableStage, TableStageToRVD}
 import is.hail.io.{exportTypes, BufferSpec, ByteArrayDecoder, ByteArrayEncoder, TypedCodecSpec}
 import is.hail.rvd.{RVD, RVDContext, RVDPartitioner, RVDType}
 import is.hail.sparkextras.ContextRDD
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical.{
   PArray, PCanonicalArray, PCanonicalStruct, PInt32Required, PStruct, PType,
 }
@@ -22,7 +26,6 @@ import is.hail.types.physical.stypes.interfaces.NoBoxLongIterator
 import is.hail.types.tcoerce
 import is.hail.types.virtual.{Field, MatrixType, TArray, TInt32, TStream, TStruct, TableType}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.reflect.ClassTag
 
@@ -49,23 +52,23 @@ sealed trait TableExecuteIntermediate {
 }
 
 case class TableValueIntermediate(tv: TableValue) extends TableExecuteIntermediate {
-  def asTableStage(ctx: ExecuteContext): TableStage =
+  override def asTableStage(ctx: ExecuteContext): TableStage =
     RVDToTableStage(tv.rvd, tv.globals.toEncodedLiteral(ctx.theHailClassLoader))
 
-  def asTableValue(ctx: ExecuteContext): TableValue = tv
+  override def asTableValue(ctx: ExecuteContext): TableValue = tv
 
-  def partitioner: RVDPartitioner = tv.rvd.partitioner
+  override def partitioner: RVDPartitioner = tv.rvd.partitioner
 }
 
 case class TableStageIntermediate(ts: TableStage) extends TableExecuteIntermediate {
-  def asTableStage(ctx: ExecuteContext): TableStage = ts
+  override def asTableStage(ctx: ExecuteContext): TableStage = ts
 
-  def asTableValue(ctx: ExecuteContext): TableValue = {
+  override def asTableValue(ctx: ExecuteContext): TableValue = {
     val (globals, rvd) = TableStageToRVD(ctx, ts)
     TableValue(ctx, TableType(ts.rowType, ts.key, ts.globalType), globals, rvd)
   }
 
-  def partitioner: RVDPartitioner = ts.partitioner
+  override def partitioner: RVDPartitioner = ts.partitioner
 }
 
 object TableValue extends Logging {
@@ -529,7 +532,7 @@ case class TableValue(ctx: ExecuteContext, typ: TableType, globals: BroadcastRow
           val rowKey: WritableRegionValue = WritableRegionValue(sm, keyType, ctx.freshRegion())
           val consumerRegion: Region = ctx.region
 
-          def hasNext: Boolean = {
+          override def hasNext: Boolean = {
             if (isEnd || (current == 0 && !it.hasNext)) {
               isEnd = true
               return false
@@ -539,7 +542,7 @@ case class TableValue(ctx: ExecuteContext, typ: TableType, globals: BroadcastRow
             true
           }
 
-          def next(): Long = {
+          override def next(): Long = {
             if (!hasNext)
               throw new java.util.NoSuchElementException()
 
@@ -641,9 +644,9 @@ case class TableValue(ctx: ExecuteContext, typ: TableType, globals: BroadcastRow
           new Iterator[Long] {
             private[this] var i = 0
 
-            def hasNext: Boolean = i < len
+            override def hasNext: Boolean = i < len
 
-            def next(): Long = {
+            override def next(): Long = {
               val ret = rowF(ctx.region, ptr, i)
               i += 1
               ret
diff --git a/hail/hail/src/is/hail/expr/ir/TableWriter.scala b/hail/hail/src/is/hail/expr/ir/TableWriter.scala
index 0cad81ba033..95e030a3138 100644
--- a/hail/hail/src/is/hail/expr/ir/TableWriter.scala
+++ b/hail/hail/src/is/hail/expr/ir/TableWriter.scala
@@ -1,9 +1,12 @@
 package is.hail.expr.ir
 
-import is.hail.GenericIndexedSeqSerializer
+import is.hail.PrettyVersion
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeOutputBuffer, valueToRichCodeRegion}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.TableAnnotationImpex
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.StringFunctions
@@ -24,12 +27,13 @@ import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.{SBooleanValue, SInt64, SInt64Value}
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.richUtils.ByteTrackingOutputStream
+import is.hail.utils.implicits.ByteTrackingOutputStream
 import is.hail.variant.ReferenceGenome
 
-import java.io.{BufferedOutputStream, OutputStream}
+import java.io.{BufferedOutputStream, OutputStream, OutputStreamWriter}
 import java.nio.file.{FileSystems, Path}
-import java.util.UUID
+import java.text.SimpleDateFormat
+import java.util.{Date, UUID}
 
 import org.json4s.{DefaultFormats, Formats, JBool, JObject, ShortTypeHints}
 
@@ -145,6 +149,17 @@ object TableNativeWriter {
       }
     )
   }
+
+  def writeFileReadMe(fs: FS, path: String): Unit = {
+    val dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss")
+    using(new OutputStreamWriter(fs.create(path + "/README.txt"))) { out =>
+      out.write(
+        s"""This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+           |  Written with version $PrettyVersion
+           |  Created at ${dateFormat.format(new Date())}""".stripMargin
+      )
+    }
+  }
 }
 
 case class TableNativeWriter(
@@ -196,10 +211,10 @@ case class PartitionNativeWriter(
 ) extends PartitionWriter {
   val keyType = spec.encodedVirtualType.asInstanceOf[TStruct].select(keyFields)._1
 
-  def ctxType = PartitionNativeWriter.ctxType
+  override def ctxType = PartitionNativeWriter.ctxType
   val returnType = PartitionNativeWriter.returnType(keyType, trackTotalBytes)
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     r: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -383,7 +398,7 @@ case class PartitionNativeWriter(
     }
   }
 
-  def consumeStream(
+  override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -402,9 +417,9 @@ case class PartitionNativeWriter(
 }
 
 case class RVDSpecWriter(path: String, spec: RVDSpecMaker) extends MetadataWriter {
-  def annotationType: Type = TArray(TString)
+  override def annotationType: Type = TArray(TString)
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -439,7 +454,7 @@ class TableSpecHelper(
   def write(fs: FS, partCounts: Array[Long], distinctlyKeyed: Boolean): Unit = {
     val spec = TableSpecParameters(
       FileFormat.version.rep,
-      is.hail.HAIL_PRETTY_VERSION,
+      is.hail.PrettyVersion,
       refRelPath,
       typ,
       Map(
@@ -469,14 +484,14 @@ case class TableSpecWriter(
   refRelPath: String,
   log: Boolean,
 ) extends MetadataWriter {
-  def annotationType: Type = TArray(TStruct(
+  override def annotationType: Type = TArray(TStruct(
     "partitionCounts" -> TInt64,
     "distinctlyKeyed" -> TBoolean,
     "firstKey" -> typ.keyType,
     "lastKey" -> typ.keyType,
   ))
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -576,9 +591,10 @@ case class RelationalSetup(path: String, overwrite: Boolean, refs: Option[TableT
     ))
   )
 
-  def annotationType: Type = TVoid
+  override def annotationType: Type = TVoid
 
-  def writeMetadata(ignored: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region]): Unit = {
+  override def writeMetadata(ignored: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
+    : Unit = {
     if (overwrite)
       cb += cb.emb.getFS.invoke[String, Boolean, Unit]("delete", path, true)
     else
@@ -605,16 +621,16 @@ case class RelationalSetup(path: String, overwrite: Boolean, refs: Option[TableT
 }
 
 case class RelationalCommit(path: String) extends MetadataWriter {
-  def annotationType: Type = TStruct()
+  override def annotationType: Type = TStruct()
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
   ): Unit = {
     cb += Code.invokeScalaObject2[FS, String, Unit](
-      Class.forName("is.hail.utils.package$"),
-      "writeNativeFileReadMe",
+      Class.forName("is.hail.expr.ir.TableNativeWriter$"),
+      "writeFileReadMe",
       cb.emb.getFS,
       path,
     )
@@ -627,9 +643,9 @@ case class RelationalWriter(
   overwrite: Boolean,
   maybeRefs: Option[(String, Set[String])],
 ) extends MetadataWriter {
-  def annotationType: Type = TVoid
+  override def annotationType: Type = TVoid
 
-  def writeMetadata(
+  override def writeMetadata(
     writeAnnotations: => IEmitCode,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -664,8 +680,8 @@ case class RelationalWriter(
     ) // PVoidCode.code is Code._empty
 
     cb += Code.invokeScalaObject2[FS, String, Unit](
-      Class.forName("is.hail.utils.package$"),
-      "writeNativeFileReadMe",
+      Class.forName("is.hail.expr.ir.TableNativeWriter$"),
+      "writeFileReadMe",
       cb.emb.getFS,
       path,
     )
@@ -734,7 +750,7 @@ case class TableTextPartitionWriter(rowType: TStruct, delimiter: String, writeHe
     cb += os.invoke[Int, Unit]("write", '\n')
   }
 
-  def consumeElement(
+  override def consumeElement(
     cb: EmitCodeBuilder,
     element: EmitCode,
     os: Value[OutputStream],
@@ -808,10 +824,13 @@ case class TableTextFinalizer(
   header: Boolean = true,
   exportType: String = ExportType.CONCATENATED,
 ) extends MetadataWriter {
-  def annotationType: Type = TArray(TString)
+  override def annotationType: Type = TArray(TString)
 
-  def writeMetadata(writeAnnotations: => IEmitCode, cb: EmitCodeBuilder, region: Value[Region])
-    : Unit = {
+  override def writeMetadata(
+    writeAnnotations: => IEmitCode,
+    cb: EmitCodeBuilder,
+    region: Value[Region],
+  ): Unit = {
     val ctx: ExecuteContext = cb.emb.ctx
     val ext = ctx.fs.getCodecExtension(outputPath)
     val partPaths = writeAnnotations.getOrFatal(cb, "write annotations cannot be missing!")
@@ -1064,7 +1083,7 @@ case class TableNativeFanoutWriter(
 class PartitionNativeFanoutWriter(
   targets: IndexedSeq[FanoutWriterTarget]
 ) extends PartitionWriter {
-  def consumeStream(
+  override def consumeStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     stream: StreamProducer,
@@ -1097,12 +1116,12 @@ class PartitionNativeFanoutWriter(
     )
   }
 
-  def ctxType = TString
+  override def ctxType = TString
 
-  def returnType: TTuple =
+  override def returnType: TTuple =
     TTuple(targets.map(target => target.rowWriter.returnType): _*)
 
-  def unionTypeRequiredness(
+  override def unionTypeRequiredness(
     returnType: TypeWithRequiredness,
     ctxType: TypeWithRequiredness,
     streamType: RIterable,
@@ -1117,8 +1136,7 @@ class PartitionNativeFanoutWriter(
 
 object WrappedMatrixNativeMultiWriter {
   implicit val formats: Formats = MatrixNativeMultiWriter.formats +
-    ShortTypeHints(List(classOf[WrappedMatrixNativeMultiWriter])) +
-    GenericIndexedSeqSerializer
+    ShortTypeHints(List(classOf[WrappedMatrixNativeMultiWriter]))
 }
 
 case class WrappedMatrixNativeMultiWriter(
diff --git a/hail/hail/src/is/hail/expr/ir/TypeCheck.scala b/hail/hail/src/is/hail/expr/ir/TypeCheck.scala
index 166014c34ba..acc56c264ec 100644
--- a/hail/hail/src/is/hail/expr/ir/TypeCheck.scala
+++ b/hail/hail/src/is/hail/expr/ir/TypeCheck.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.implicits.{toRichIterable, toRichOrderedSeq}
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.streams.StreamUtils
@@ -323,6 +324,8 @@ object TypeCheck {
           case t => t == TInt64
         }
         assert(isValid(dynBitstring.typ))
+      case RNGSplitStatic(state, _) =>
+        assert(state.typ == TRNGState)
       case StreamLen(a) =>
         assert(a.typ.isInstanceOf[TStream])
       case x @ StreamTake(a, num) =>
diff --git a/hail/hail/src/is/hail/expr/ir/ValueReader.scala b/hail/hail/src/is/hail/expr/ir/ValueReader.scala
index 0305502b818..0a887a68738 100644
--- a/hail/hail/src/is/hail/expr/ir/ValueReader.scala
+++ b/hail/hail/src/is/hail/expr/ir/ValueReader.scala
@@ -2,11 +2,14 @@ package is.hail.expr.ir
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
-import is.hail.io.{AbstractTypedCodecSpec, BufferSpec, TypedCodecSpec}
+import is.hail.asm4s.implicits._
+import is.hail.io.{AbstractTypedCodecSpec, BufferSpec, StreamBufferSpec, TypedCodecSpec}
 import is.hail.types.TypeWithRequiredness
 import is.hail.types.encoded._
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.SValue
+import is.hail.types.physical.stypes.concrete.SNDArrayPointer
+import is.hail.types.physical.stypes.primitives.SFloat64Value
 import is.hail.types.virtual._
 
 import java.io.InputStream
@@ -19,6 +22,7 @@ object ValueReader {
       override val typeHints = ShortTypeHints(
         List(
           classOf[ETypeValueReader],
+          classOf[NumpyBinaryValueReader],
           classOf[AbstractTypedCodecSpec],
           classOf[TypedCodecSpec],
         ),
@@ -40,14 +44,56 @@ abstract class ValueReader {
 }
 
 final case class ETypeValueReader(spec: AbstractTypedCodecSpec) extends ValueReader {
-  def unionRequiredness(requestedType: Type, requiredness: TypeWithRequiredness): Unit =
+  override def unionRequiredness(requestedType: Type, requiredness: TypeWithRequiredness): Unit =
     requiredness.fromPType(spec.encodedType.decodedPType(requestedType))
 
-  def readValue(cb: EmitCodeBuilder, t: Type, region: Value[Region], is: Value[InputStream])
-    : SValue = {
+  override def readValue(
+    cb: EmitCodeBuilder,
+    t: Type,
+    region: Value[Region],
+    is: Value[InputStream],
+  ): SValue = {
     val decoder = spec.encodedType.buildDecoder(t, cb.emb.ecb)
     val ib = cb.memoize(spec.buildCodeInputBuffer(is))
     val ret = decoder.apply(cb, region, ib)
     ret
   }
 }
+
+final case class NumpyBinaryValueReader(nRows: Long, nCols: Long) extends ValueReader {
+  final private val st = SNDArrayPointer(PCanonicalNDArray(PFloat64(true), 2, false))
+
+  override def unionRequiredness(requestedType: Type, requiredness: TypeWithRequiredness): Unit =
+    requiredness.fromPType(st.pType.setRequired(true))
+
+  override def readValue(
+    cb: EmitCodeBuilder,
+    t: Type,
+    region: Value[Region],
+    is: Value[InputStream],
+  ): SValue = {
+    val pt = st.pType
+
+    val stride0 = const(nCols * pt.elementType.byteSize)
+    val stride1 = const(pt.elementType.byteSize)
+
+    val in = cb.memoize(new StreamBufferSpec().buildCodeInputBuffer(is))
+    val (tFirstElementAddress, tFinisher) =
+      pt.constructDataFunction(IndexedSeq(nRows, nCols), IndexedSeq(stride0, stride1), cb, region)
+    val currElementAddress =
+      cb.newLocal[Long]("eblockmatrix_ndarray_currElementAddress", tFirstElementAddress)
+
+    val i = cb.newLocal[Long]("i")
+    cb.for_(
+      cb.assign(i, 0L),
+      i < nRows * nCols,
+      cb.assign(i, i + 1L), {
+        val elem = SFloat64Value(cb.memoize(in.readDouble()))
+        pt.elementType.storeAtAddress(cb, currElementAddress, region, elem, false)
+        cb.assign(currElementAddress, currElementAddress + pt.elementType.byteSize)
+      },
+    )
+
+    tFinisher(cb)
+  }
+}
diff --git a/hail/hail/src/is/hail/expr/ir/ValueWriter.scala b/hail/hail/src/is/hail/expr/ir/ValueWriter.scala
index 1205006008c..e3bb09eedf5 100644
--- a/hail/hail/src/is/hail/expr/ir/ValueWriter.scala
+++ b/hail/hail/src/is/hail/expr/ir/ValueWriter.scala
@@ -1,10 +1,13 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s._
-import is.hail.io.{AbstractTypedCodecSpec, BufferSpec, TypedCodecSpec}
+import is.hail.asm4s.implicits._
+import is.hail.collection.FastSeq
+import is.hail.io.{AbstractTypedCodecSpec, BufferSpec, StreamBufferSpec, TypedCodecSpec}
 import is.hail.types.encoded._
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.SValue
+import is.hail.types.physical.stypes.primitives.SFloat64
 import is.hail.types.virtual._
 
 import java.io.OutputStream
@@ -17,6 +20,7 @@ object ValueWriter {
       override val typeHints = ShortTypeHints(
         List(
           classOf[ETypeValueWriter],
+          classOf[NumpyBinaryValueWriter],
           classOf[AbstractTypedCodecSpec],
           classOf[TypedCodecSpec],
         ),
@@ -36,10 +40,34 @@ abstract class ValueWriter {
 }
 
 final case class ETypeValueWriter(spec: AbstractTypedCodecSpec) extends ValueWriter {
-  def writeValue(cb: EmitCodeBuilder, value: SValue, os: Value[OutputStream]): Unit = {
+  override def writeValue(cb: EmitCodeBuilder, value: SValue, os: Value[OutputStream]): Unit = {
     val encoder = spec.encodedType.buildEncoder(value.st, cb.emb.ecb)
     val ob = cb.memoize(spec.buildCodeOutputBuffer(os))
     encoder.apply(cb, value, ob)
     cb += ob.invoke[Unit]("flush")
   }
 }
+
+final case class NumpyBinaryValueWriter(nRows: Long, nCols: Long) extends ValueWriter {
+  override def writeValue(cb: EmitCodeBuilder, value: SValue, os: Value[OutputStream]): Unit = {
+    val ob = cb.memoize(new StreamBufferSpec().buildCodeOutputBuffer(os))
+    val ndarray = value.asNDArray
+    assert(ndarray.st.elementType == SFloat64)
+    val i = cb.newLocal[Long]("i")
+    val j = cb.newLocal[Long]("j")
+
+    cb.for_(
+      cb.assign(i, 0L),
+      i < nRows,
+      cb.assign(i, i + 1L),
+      cb.for_(
+        cb.assign(j, 0L),
+        j < nCols,
+        cb.assign(j, j + 1L),
+        cb += ob.writeDouble(ndarray.loadElement(FastSeq(i, j), cb).asFloat64.value),
+      ),
+    )
+
+    cb += ob.invoke[Unit]("flush")
+  }
+}
diff --git a/hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala b/hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala
index b65cdb663aa..f1a4c9b520b 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/AggregatorState.scala
@@ -2,6 +2,9 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.expr.ir._
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer, TypedCodecSpec}
 import is.hail.types.VirtualTypeWithReq
@@ -75,19 +78,19 @@ trait RegionBackedAggState extends AggregatorState {
   protected val r: Settable[Region] = kb.genFieldThisRef[Region]()
   val region: Value[Region] = r
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
     cb += region.getNewRegion(const(regionSize))
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
 
-  def load(
+  override def load(
     cb: EmitCodeBuilder,
     regionLoader: (EmitCodeBuilder, Value[Region]) => Unit,
     src: Value[Long],
   ): Unit = regionLoader(cb, r)
 
-  def store(
+  override def store(
     cb: EmitCodeBuilder,
     regionStorer: (EmitCodeBuilder, Value[Region]) => Unit,
     dest: Value[Long],
@@ -127,7 +130,7 @@ trait PointerBasedRVAState extends RegionBackedAggState {
       },
     )
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit =
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit =
     copyFromAddress(cb, cb.memoize(Region.loadAddress(src)))
 
   def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit
@@ -189,7 +192,7 @@ abstract class AbstractTypedRegionBackedAggState(val ptype: PType) extends Regio
       ptype.loadCheapSCode(cb, storageType.loadField(off, 0)),
     )
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     newState(cb, off)
     storageType.storeAtAddress(
       cb,
@@ -200,13 +203,13 @@ abstract class AbstractTypedRegionBackedAggState(val ptype: PType) extends Regio
     )
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     val codecSpec = TypedCodecSpec(kb.ctx, storageType, codec)
     val enc = codecSpec.encodedType.buildEncoder(storageType.sType, kb)
     (cb, ob: Value[OutputBuffer]) => enc(cb, storageType.loadCheapSCode(cb, off), ob)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val codecSpec = TypedCodecSpec(kb.ctx, storageType, codec)
 
     val dec = codecSpec.encodedType.buildDecoder(storageType.virtualType, kb)
@@ -232,23 +235,23 @@ class PrimitiveRVAState(val vtypes: Array[VirtualTypeWithReq], val kb: EmitClass
   def foreachField(f: (Int, EmitSettable) => Unit): Unit =
     (0 until nFields).foreach(i => f(i, fields(i)))
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = {}
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = {}
 
-  def createState(cb: EmitCodeBuilder): Unit = {}
+  override def createState(cb: EmitCodeBuilder): Unit = {}
 
   private[this] def loadVarsFromRegion(cb: EmitCodeBuilder, srcc: Code[Long]): Unit = {
     val pv = storageType.loadCheapSCode(cb, srcc)
     foreachField((i, es) => cb.assign(es, pv.loadField(cb, i)))
   }
 
-  def load(
+  override def load(
     cb: EmitCodeBuilder,
     regionLoader: (EmitCodeBuilder, Value[Region]) => Unit,
     src: Value[Long],
   ): Unit =
     loadVarsFromRegion(cb, src)
 
-  def store(
+  override def store(
     cb: EmitCodeBuilder,
     regionStorer: (EmitCodeBuilder, Value[Region]) => Unit,
     dest: Value[Long],
@@ -261,9 +264,9 @@ class PrimitiveRVAState(val vtypes: Array[VirtualTypeWithReq], val kb: EmitClass
       false,
     )
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = loadVarsFromRegion(cb, src)
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = loadVarsFromRegion(cb, src)
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb, ob: Value[OutputBuffer]) =>
       foreachField { case (_, es) =>
         if (es.emitType.required) {
@@ -281,7 +284,7 @@ class PrimitiveRVAState(val vtypes: Array[VirtualTypeWithReq], val kb: EmitClass
       }
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb, ib: Value[InputBuffer]) =>
       foreachField { case (_, es) =>
         if (es.emitType.required) {
diff --git a/hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala b/hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala
index a1411542107..744974ff254 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/AppendOnlyBTree.scala
@@ -2,10 +2,13 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
-import is.hail.utils._
 
 trait BTreeKey {
   def storageType: PType
@@ -18,7 +21,7 @@ trait BTreeKey {
 
   def copy(cb: EmitCodeBuilder, src: Code[Long], dest: Code[Long]): Unit
 
-  def deepCopy(cb: EmitCodeBuilder, er: EmitRegion, src: Code[Long], dest: Code[Long]): Unit
+  def deepCopy(cb: EmitCodeBuilder, r: Value[Region], src: Code[Long], dest: Code[Long]): Unit
 
   def compKeys(cb: EmitCodeBuilder, k1: EmitValue, k2: EmitValue): Value[Int]
 
@@ -430,7 +433,6 @@ class AppendOnlyBTree(
         val destNode = f.getCodeParam[Long](1)
         val srcNode = f.getCodeParam[Long](2)
 
-        val er = EmitRegion(cb.emb, region)
         val newNode = cb.newLocal[Long]("new_node")
 
         def copyChild(i: Int): Unit = {
@@ -448,7 +450,7 @@ class AppendOnlyBTree(
         (0 until maxElements).foreach { i =>
           cb.if_(
             hasKey(cb, srcNode, i), {
-              key.deepCopy(cb, er, destNode, srcNode)
+              key.deepCopy(cb, region, destNode, srcNode)
               cb.if_(
                 !isLeaf(cb, srcNode), {
                   copyChild(i)
diff --git a/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
index 9d68f82e47b..0be2fbfdeed 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFAggregator.scala
@@ -2,14 +2,17 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.{SBaseStructPointer, SBaseStructPointerValue}
 import is.hail.types.virtual.{TFloat64, TInt32, Type}
-import is.hail.utils._
 
 class ApproxCDFState(val kb: EmitClassBuilder[_]) extends AggregatorState {
   override val regionSize: Region.Size = Region.TINIER
@@ -61,9 +64,10 @@ class ApproxCDFState(val kb: EmitClassBuilder[_]) extends AggregatorState {
       aggr.invoke[Region, Long]("rvResult", region),
     )
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = cb += region.getNewRegion(regionSize)
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+    cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
 
   override def load(
@@ -144,11 +148,13 @@ class ApproxCDFState(val kb: EmitClassBuilder[_]) extends AggregatorState {
 class ApproxCDFAggregator extends StagedAggregator {
   type State = ApproxCDFState
 
-  def resultEmitType: EmitType = EmitType(SBaseStructPointer(QuantilesAggregator.resultPType), true)
+  override def resultEmitType: EmitType =
+    EmitType(SBaseStructPointer(QuantilesAggregator.resultPType), true)
+
   val initOpTypes: Seq[Type] = FastSeq(TInt32)
   val seqOpTypes: Seq[Type] = FastSeq(TFloat64)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     val Array(k) = init
     k.toI(cb)
       .consume(
@@ -158,7 +164,7 @@ class ApproxCDFAggregator extends StagedAggregator {
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(x) = seq
     x.toI(cb)
       .consume(
@@ -168,7 +174,7 @@ class ApproxCDFAggregator extends StagedAggregator {
       )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -177,6 +183,7 @@ class ApproxCDFAggregator extends StagedAggregator {
   ): Unit =
     state.comb(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     IEmitCode.present(cb, state.result(cb, region))
 }
diff --git a/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
index ad7bfdb2c30..fd5a21c9349 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/ApproxCDFStateManager.scala
@@ -2,12 +2,11 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
-import is.hail.expr.ir.{DoubleArrayBuilder, IntArrayBuilder, LongArrayBuilder}
+import is.hail.collection.{DoubleArrayBuilder, IntArrayBuilder, LongArrayBuilder}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichArraySeqCompanion
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.{PCanonicalArray, PCanonicalStruct, PFloat64, PInt32}
-import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 object ApproxCDFHelper {
   def sort(a: Array[Double], begin: Int, end: Int): Unit = java.util.Arrays.sort(a, begin, end)
diff --git a/hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
index 580b3050214..6c518877a77 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/ArrayElementLengthCheckAggregator.scala
@@ -2,14 +2,17 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{coerce => _, _}
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SValue}
 import is.hail.types.physical.stypes.concrete.SIndexablePointer
 import is.hail.types.virtual.{TInt32, TVoid, Type}
-import is.hail.utils._
 
 // initOp args: initOps for nestedAgg, length if knownLength = true
 // seqOp args: array, other non-elt args for nestedAgg
@@ -27,11 +30,11 @@ class ArrayElementState(val kb: EmitClassBuilder[_], val nested: StateTuple)
   private val aoff: Settable[Long] = kb.genFieldThisRef[Long]("arrayrva_aoff")
 
   private def regionOffset(eltIdx: Value[Int]): Value[Int] = new Value[Int] {
-    def get: Code[Int] = (eltIdx + 1) * nStates
+    override def get: Code[Int] = (eltIdx + 1) * nStates
   }
 
   private def statesOffset(eltIdx: Value[Int]): Value[Long] = new Value[Long] {
-    def get: Code[Long] = arrayType.loadElement(typ.loadField(off, 1), eltIdx)
+    override def get: Code[Long] = arrayType.loadElement(typ.loadField(off, 1), eltIdx)
   }
 
   val initContainer: TupleAggregatorState = new TupleAggregatorState(
@@ -39,7 +42,7 @@ class ArrayElementState(val kb: EmitClassBuilder[_], val nested: StateTuple)
     nested,
     region,
     new Value[Long] {
-      def get: Code[Long] = typ.loadField(off, 0)
+      override def get: Code[Long] = typ.loadField(off, 0)
     },
   )
 
@@ -118,7 +121,7 @@ class ArrayElementState(val kb: EmitClassBuilder[_], val nested: StateTuple)
 
   def store(cb: EmitCodeBuilder): Unit = container.store(cb)
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     val serializers = nested.states.map(_.serialize(codec));
     { (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       loadInit(cb)
@@ -140,7 +143,7 @@ class ArrayElementState(val kb: EmitClassBuilder[_], val nested: StateTuple)
     }
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val deserializers = nested.states.map(_.deserialize(codec));
     { (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
       init(
@@ -157,7 +160,7 @@ class ArrayElementState(val kb: EmitClassBuilder[_], val nested: StateTuple)
     }
   }
 
-  def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     init(cb, cb => initContainer.copyFrom(cb, cb.memoize(typ.loadField(src, 0))), initLen = false)
     cb.if_(
       typ.isFieldMissing(cb, src, 1), {
@@ -188,7 +191,7 @@ class ArrayElementLengthCheckAggregator(nestedAggs: Array[StagedAggregator], kno
   val seqOpTypes: Seq[Type] = FastSeq(TInt32)
 
   // inits all things
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     if (knownLength) {
       val Array(len, inits) = init
       state.init(cb, cb => cb += inits.asVoid(), initLen = false)
@@ -205,7 +208,7 @@ class ArrayElementLengthCheckAggregator(nestedAggs: Array[StagedAggregator], kno
   }
 
   // does a length check on arrays
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     assert(seq.length == 1)
     val len = seq.head
     len.toI(cb).consume(
@@ -223,7 +226,7 @@ class ArrayElementLengthCheckAggregator(nestedAggs: Array[StagedAggregator], kno
     )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -312,12 +315,12 @@ class ArrayElementwiseOpAggregator(nestedAggs: Array[StagedAggregator]) extends
 
   override def resultEmitType = EmitType(SIndexablePointer(resultPType), false)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit =
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit =
     throw new UnsupportedOperationException(
       "State must be initialized by ArrayElementLengthCheckAggregator."
     )
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(eltIdx, seqOps) = seq
     eltIdx.toI(cb).consume(
       cb,
@@ -336,7 +339,7 @@ class ArrayElementwiseOpAggregator(nestedAggs: Array[StagedAggregator]) extends
     )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -347,7 +350,8 @@ class ArrayElementwiseOpAggregator(nestedAggs: Array[StagedAggregator]) extends
       "State must be combined by ArrayElementLengthCheckAggregator."
     )
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     throw new UnsupportedOperationException(
       "Result must be defined by ArrayElementLengthCheckAggregator."
     )
diff --git a/hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala
index 4720c29a8a5..abecbb1aafd 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/CallStatsAggregator.scala
@@ -2,7 +2,9 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer, TypedCodecSpec}
 import is.hail.types.physical._
@@ -10,7 +12,6 @@ import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.SBaseStructPointer
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.{TCall, TInt32, Type}
-import is.hail.utils._
 
 object CallStatsState {
   val callStatsInternalArrayType = PCanonicalArray(PInt32Required, required = true)
@@ -97,13 +98,14 @@ class CallStatsState(val kb: EmitClassBuilder[_]) extends PointerBasedRVAState {
     cb += Region.storeInt(addr, updater(Region.loadInt(addr)))
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = { (cb, ob) =>
-    val codecSpec = TypedCodecSpec(kb.ctx, CallStatsState.stateType, codec)
-    codecSpec.encodedType.buildEncoder(CallStatsState.stateType.sType, kb)
-      .apply(cb, CallStatsState.stateType.loadCheapSCode(cb, off), ob)
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+    (cb, ob) =>
+      val codecSpec = TypedCodecSpec(kb.ctx, CallStatsState.stateType, codec)
+      codecSpec.encodedType.buildEncoder(CallStatsState.stateType.sType, kb)
+        .apply(cb, CallStatsState.stateType.loadCheapSCode(cb, off), ob)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
       val codecSpec = TypedCodecSpec(kb.ctx, CallStatsState.stateType, codec)
       val decValue = codecSpec.encodedType.buildDecoder(CallStatsState.stateType.virtualType, kb)
@@ -113,7 +115,7 @@ class CallStatsState(val kb: EmitClassBuilder[_]) extends PointerBasedRVAState {
       loadNAlleles(cb)
   }
 
-  def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     cb.assign(
       off,
       CallStatsState.stateType.store(
@@ -137,7 +139,7 @@ class CallStatsAggregator extends StagedAggregator {
   val initOpTypes: Seq[Type] = FastSeq(TInt32)
   val seqOpTypes: Seq[Type] = FastSeq(TCall)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     val Array(nAlleles) = init
     val addr = state.kb.genFieldThisRef[Long]()
     val n = state.kb.genFieldThisRef[Int]()
@@ -175,7 +177,7 @@ class CallStatsAggregator extends StagedAggregator {
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(call) = seq
 
     call.toI(cb).consume(
@@ -203,7 +205,7 @@ class CallStatsAggregator extends StagedAggregator {
     )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -236,7 +238,8 @@ class CallStatsAggregator extends StagedAggregator {
     )
   }
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     val rt = CallStatsState.resultPType
     val addr = cb.memoize(rt.allocate(region), "call_stats_aggregator_result_addr")
     rt.stagedInitialize(cb, addr, setMissing = false)
diff --git a/hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala
index 907fa809639..789bc748daa 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/CollectAggregator.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.ExecuteContext
 import is.hail.expr.ir._
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
@@ -10,7 +11,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.SIndexablePointer
 import is.hail.types.virtual.Type
-import is.hail.utils._
 
 class CollectAggState(val elemVType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
     extends AggregatorState {
@@ -20,11 +20,11 @@ class CollectAggState(val elemVType: VirtualTypeWithReq, val kb: EmitClassBuilde
   val region: Value[Region] = r
   val bll = new StagedBlockLinkedList(elemType, kb)
 
-  def storageType = bll.storageType
+  override def storageType = bll.storageType
 
   override def regionSize: Region.Size = Region.REGULAR
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(
       region.isNull, {
         cb.assign(r, Region.stagedCreate(regionSize, kb.pool()))
@@ -32,7 +32,8 @@ class CollectAggState(val elemVType: VirtualTypeWithReq, val kb: EmitClassBuilde
       },
     )
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = cb += region.getNewRegion(regionSize)
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+    cb += region.getNewRegion(regionSize)
 
   override def load(
     cb: EmitCodeBuilder,
@@ -57,17 +58,17 @@ class CollectAggState(val elemVType: VirtualTypeWithReq, val kb: EmitClassBuilde
     )
   }
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     val copyBll = new StagedBlockLinkedList(elemType, kb)
     copyBll.load(cb, src)
     bll.initWithDeepCopy(cb, region, copyBll)
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb, ib) => bll.serialize(cb, region, ib)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb, ib) =>
       bll.init(cb, region)
       bll.deserialize(cb, region, ib)
@@ -82,15 +83,15 @@ class CollectAggregator(val elemType: VirtualTypeWithReq) extends StagedAggregat
   val initOpTypes: Seq[Type] = Array[Type]()
   val seqOpTypes: Seq[Type] = Array[Type](elemType.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, args: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, args: Array[EmitCode]): Unit = {
     assert(args.isEmpty)
     state.bll.init(cb, state.region)
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit =
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit =
     state.bll.push(cb, state.region, seq(0))
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -99,7 +100,8 @@ class CollectAggregator(val elemType: VirtualTypeWithReq) extends StagedAggregat
   ): Unit =
     state.bll.append(cb, state.region, other.bll)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     // deepCopy is handled by the blocked linked list
     IEmitCode.present(
       cb,
diff --git a/hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
index 6eade3802fd..3625d7d6d0c 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/CollectAsSetAggregator.scala
@@ -2,10 +2,11 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
-import is.hail.backend.ExecuteContext
-import is.hail.expr.ir.{
-  EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitRegion, EmitValue, IEmitCode,
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
 }
+import is.hail.backend.ExecuteContext
+import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitValue, IEmitCode}
 import is.hail.expr.ir.orderings.CodeOrdering
 import is.hail.io._
 import is.hail.types.VirtualTypeWithReq
@@ -14,7 +15,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SValue}
 import is.hail.types.physical.stypes.concrete.SIndexablePointer
 import is.hail.types.virtual.Type
-import is.hail.utils._
 
 class TypedKey(typ: PType, kb: EmitClassBuilder[_], region: Value[Region]) extends BTreeKey {
   override val storageType: PTuple = PCanonicalTuple(false, typ, PCanonicalTuple(false))
@@ -50,7 +50,7 @@ class TypedKey(typ: PType, kb: EmitClassBuilder[_], region: Value[Region]) exten
   override def copy(cb: EmitCodeBuilder, src: Code[Long], dest: Code[Long]): Unit =
     cb += Region.copyFrom(src, dest, storageType.byteSize)
 
-  override def deepCopy(cb: EmitCodeBuilder, er: EmitRegion, dest: Code[Long], src: Code[Long])
+  override def deepCopy(cb: EmitCodeBuilder, r: Value[Region], dest: Code[Long], src: Code[Long])
     : Unit =
     storageType.storeAtAddress(
       cb,
@@ -137,14 +137,14 @@ class AppendOnlySetState(val kb: EmitClassBuilder[_], vt: VirtualTypeWithReq)
       )
     }
 
-  def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     cb.assign(off, region.allocate(typ.alignment, typ.byteSize))
     cb.assign(size, Region.loadInt(typ.loadField(src, 0)))
     tree.init(cb)
     tree.deepCopy(cb, cb.memoize(Region.loadAddress(typ.loadField(src, 1))))
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       tree.bulkStore(cb, ob) { (cb, ob, srcCode) =>
         val src = cb.newLocal("aoss_ser_src", srcCode)
@@ -159,7 +159,7 @@ class AppendOnlySetState(val kb: EmitClassBuilder[_], vt: VirtualTypeWithReq)
       }
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val kDec = et.buildDecoder(t.virtualType, kb)
 
     { (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
@@ -184,17 +184,17 @@ class CollectAsSetAggregator(elem: VirtualTypeWithReq) extends StagedAggregator
   val initOpTypes: Seq[Type] = Array[Type]()
   val seqOpTypes: Seq[Type] = Array[Type](elem.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 0)
     state.init(cb)
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(elt) = seq
     state.insert(cb, elt)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -203,7 +203,8 @@ class CollectAsSetAggregator(elem: VirtualTypeWithReq) extends StagedAggregator
   ): Unit =
     other.foreach(cb)((cb, k) => state.insert(cb, k))
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     val (pushElement, finish) =
       arrayRep.constructFromFunctions(cb, region, state.size, deepCopy = true)
     state.foreach(cb)((cb, elt) => pushElement(cb, elt.toI(cb)))
diff --git a/hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala
index c0b447de0cb..ddf66942058 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/CountAggregator.scala
@@ -16,21 +16,21 @@ object CountAggregator extends StagedAggregator {
   val initOpTypes: Seq[Type] = Array[Type]()
   val seqOpTypes: Seq[Type] = Array[Type]()
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 0)
     assert(state.vtypes.head.r.required)
     val ev = state.fields(0)
     cb.assign(ev, EmitCode.present(cb.emb, primitive(const(0L))))
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     assert(seq.length == 0)
     assert(state.vtypes.head.r.required)
     val ev = state.fields(0)
     cb.assign(ev, EmitCode.present(cb.emb, primitive(cb.memoize(ev.pv.asInt64.value + 1L))))
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -46,7 +46,8 @@ object CountAggregator extends StagedAggregator {
     )
   }
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     assert(state.vtypes.head.r.required)
     val ev = state.fields(0)
     ev.toI(cb).map(cb)(sv => sv.copyToRegion(cb, region, sv.st))
diff --git a/hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala
index 760701c5355..81628ecb50b 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/DensifyAggregator.scala
@@ -2,6 +2,9 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer, TypedCodecSpec}
@@ -11,7 +14,6 @@ import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
 import is.hail.types.virtual.{TInt32, Type}
-import is.hail.utils._
 
 object DensifyAggregator {
   val END_SERIALIZATION: Int = 0xf81ea4
@@ -34,10 +36,10 @@ class DensifyState(val arrayVType: VirtualTypeWithReq, val kb: EmitClassBuilder[
   private val length = kb.genFieldThisRef[Int]("densify_len")
   private val arrayAddr = kb.genFieldThisRef[Long]("densify_addr")
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
     cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
 
   override def load(
@@ -60,7 +62,7 @@ class DensifyState(val arrayVType: VirtualTypeWithReq, val kb: EmitClassBuilder[
     cb += Region.storeAddress(dest, arrayAddr)
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     val codecSpec = TypedCodecSpec(kb.ctx, arrayStorageType, codec)
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) => {
 
@@ -71,7 +73,7 @@ class DensifyState(val arrayVType: VirtualTypeWithReq, val kb: EmitClassBuilder[
     }
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val codecSpec = TypedCodecSpec(kb.ctx, arrayStorageType, codec)
 
     (cb: EmitCodeBuilder, ib: Value[InputBuffer]) => {
@@ -155,7 +157,7 @@ class DensifyState(val arrayVType: VirtualTypeWithReq, val kb: EmitClassBuilder[
   def result(cb: EmitCodeBuilder, region: Value[Region]): SIndexablePointerValue =
     arrayStorageType.loadCheapSCode(cb, arrayAddr)
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     cb.assign(
       arrayAddr,
       arrayStorageType.store(
@@ -183,7 +185,7 @@ class DensifyAggregator(val arrayVType: VirtualTypeWithReq) extends StagedAggreg
   val initOpTypes: Seq[Type] = Array(TInt32)
   val seqOpTypes: Seq[Type] = Array(resultEmitType.virtualType)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 1)
     val Array(sizeTriplet) = init
     sizeTriplet.toI(cb)
@@ -194,12 +196,12 @@ class DensifyAggregator(val arrayVType: VirtualTypeWithReq) extends StagedAggreg
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(elt: EmitCode) = seq
     state.seqOp(cb, elt)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -207,7 +209,8 @@ class DensifyAggregator(val arrayVType: VirtualTypeWithReq) extends StagedAggreg
     other: DensifyState,
   ): Unit = state.combine(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     val resultInWrongRegion = state.result(cb, region)
     // deepCopy needs to be done here
     val ptrInRightRegion = pt.store(cb, region, resultInWrongRegion, true)
diff --git a/hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala
index 1b4a3f79b6b..1ad4e05792c 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/DownsampleAggregator.scala
@@ -2,9 +2,13 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
-  EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitRegion, EmitValue, IEmitCode, ParamType,
+  EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitValue, IEmitCode, ParamType,
 }
 import is.hail.expr.ir.orderings.CodeOrdering
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
@@ -15,7 +19,6 @@ import is.hail.types.physical.stypes.{EmitType, SingleCodeSCode}
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
 import is.hail.types.virtual._
-import is.hail.utils._
 
 class DownsampleBTreeKey(binType: PBaseStruct, pointType: PBaseStruct, kb: EmitClassBuilder[_])
     extends BTreeKey {
@@ -38,7 +41,7 @@ class DownsampleBTreeKey(binType: PBaseStruct, pointType: PBaseStruct, kb: EmitC
   override def copy(cb: EmitCodeBuilder, src: Code[Long], dest: Code[Long]): Unit =
     cb += Region.copyFrom(src, dest, storageType.byteSize)
 
-  override def deepCopy(cb: EmitCodeBuilder, er: EmitRegion, srcc: Code[Long], dest: Code[Long])
+  override def deepCopy(cb: EmitCodeBuilder, r: Value[Region], srcc: Code[Long], dest: Code[Long])
     : Unit = {
     val src = cb.newLocal[Long]("dsa_deep_copy_src", srcc)
     cb.if_(
@@ -48,7 +51,7 @@ class DownsampleBTreeKey(binType: PBaseStruct, pointType: PBaseStruct, kb: EmitC
     storageType.storeAtAddress(
       cb,
       dest,
-      er.region,
+      r,
       storageType.loadCheapSCode(cb, src),
       deepCopy = true,
     )
@@ -76,9 +79,10 @@ class DownsampleState(
 
   val oldRegion: Settable[Region] = kb.genFieldThisRef[Region]("old_region")
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = cb += region.getNewRegion(regionSize)
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+    cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
 
   val binType = PCanonicalStruct(required = true, "x" -> PInt32Required, "y" -> PInt32Required)
@@ -216,7 +220,7 @@ class DownsampleState(
     )
   }
 
-  def copyFrom(cb: EmitCodeBuilder, _src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, _src: Value[Long]): Unit = {
     val mb = kb.genEmitMethod("downsample_copy", FastSeq[ParamType](LongInfo), UnitInfo)
 
     val src = mb.getCodeParam[Long](1)
@@ -235,7 +239,7 @@ class DownsampleState(
     cb.invokeVoid(mb, cb.this_, _src)
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       val mb = kb.genEmitMethod(
         "downsample_serialize",
@@ -268,7 +272,7 @@ class DownsampleState(
       cb.invokeVoid(mb, cb.this_, ob)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val binDec = binET.buildInplaceDecoderMethod(binType, kb)
     val pointDec = pointET.buildInplaceDecoderMethod(pointType, kb)
 
@@ -721,7 +725,7 @@ class DownsampleAggregator(arrayType: VirtualTypeWithReq) extends StagedAggregat
   val initOpTypes: Seq[Type] = Array(TInt32)
   val seqOpTypes: Seq[Type] = Array(TFloat64, TFloat64, arrayType.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     val Array(nDivisions) = init
     nDivisions.toI(cb)
       .consume(
@@ -731,13 +735,13 @@ class DownsampleAggregator(arrayType: VirtualTypeWithReq) extends StagedAggregat
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(x, y, label) = seq
 
     state.insert(cb, x, y, label)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -745,7 +749,8 @@ class DownsampleAggregator(arrayType: VirtualTypeWithReq) extends StagedAggregat
     other: DownsampleState,
   ): Unit = state.merge(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     // deepCopy is handled by state.resultArray
     IEmitCode.present(cb, state.resultArray(cb, region, resultPType))
 }
diff --git a/hail/hail/src/is/hail/expr/ir/agg/Extract.scala b/hail/hail/src/is/hail/expr/ir/agg/Extract.scala
index 25d19feb546..814066bc546 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/Extract.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/Extract.scala
@@ -1,9 +1,13 @@
 package is.hail.expr.ir.agg
 
 import is.hail.annotations.{Region, RegionPool, RegionValue}
-import is.hail.asm4s.{HailClassLoader, _}
+import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailTaskContext}
 import is.hail.backend.spark.SparkTaskContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.compat.mutable.Growable
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir
 import is.hail.expr.ir._
 import is.hail.expr.ir.compile.CompileWithAggregators
@@ -12,10 +16,6 @@ import is.hail.io.BufferSpec
 import is.hail.types.{tcoerce, TypeWithRequiredness, VirtualTypeWithReq}
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.virtual._
-import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.compat.mutable.Growable
 
 import scala.collection.mutable
 import scala.collection.mutable.ArrayBuffer
diff --git a/hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala
index c1ce565ad86..3fc21377937 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/GroupedAggregator.scala
@@ -2,9 +2,13 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
-  EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitRegion, EmitValue, IEmitCode, ParamType,
+  EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitValue, IEmitCode, ParamType,
 }
 import is.hail.expr.ir.orderings.CodeOrdering
 import is.hail.io._
@@ -14,7 +18,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SValue}
 import is.hail.types.physical.stypes.concrete.SIndexablePointer
 import is.hail.types.virtual.{TVoid, Type}
-import is.hail.utils._
 
 class GroupedBTreeKey(
   kt: PType,
@@ -51,7 +54,7 @@ class GroupedBTreeKey(
   }
 
   val regionIdx: Value[Int] = new Value[Int] {
-    def get: Code[Int] = Region.loadInt(storageType.fieldOffset(offset, 1))
+    override def get: Code[Int] = Region.loadInt(storageType.fieldOffset(offset, 1))
   }
 
   val container = new TupleAggregatorState(kb, states, region, containerOffset(offset), regionIdx)
@@ -89,7 +92,7 @@ class GroupedBTreeKey(
     cb += Region.storeInt(storageType.fieldOffset(off, 1), idx)
 
   def containerOffset(off: Value[Long]): Value[Long] = new Value[Long] {
-    def get: Code[Long] = storageType.fieldOffset(off, 2)
+    override def get: Code[Long] = storageType.fieldOffset(off, 2)
   }
 
   override def isEmpty(cb: EmitCodeBuilder, off: Code[Long]): Value[Boolean] =
@@ -107,8 +110,12 @@ class GroupedBTreeKey(
       deepCopy = false,
     )
 
-  override def deepCopy(cb: EmitCodeBuilder, er: EmitRegion, dest: Code[Long], srcCode: Code[Long])
-    : Unit = {
+  override def deepCopy(
+    cb: EmitCodeBuilder,
+    r: Value[Region],
+    dest: Code[Long],
+    srcCode: Code[Long],
+  ): Unit = {
     val src = cb.newLocal("ga_deep_copy_src", srcCode)
     storageType.storeAtAddress(
       cb,
@@ -153,7 +160,7 @@ class DictState(
   private val _elt = kb.genFieldThisRef[Long]()
 
   private val initStatesOffset: Value[Long] = new Value[Long] {
-    def get: Code[Long] = typ.loadField(off, 0)
+    override def get: Code[Long] = typ.loadField(off, 0)
   }
 
   val initContainer: TupleAggregatorState =
@@ -246,13 +253,13 @@ class DictState(
       )
     }
 
-  def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFromAddress(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     init(cb, cb => initContainer.copyFrom(cb, cb.memoize(typ.loadField(src, 0))))
     cb.assign(size, Region.loadInt(typ.loadField(src, 1)))
     tree.deepCopy(cb, cb.memoize(Region.loadAddress(typ.loadField(src, 2))))
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     val serializers = nested.states.map(_.serialize(codec))
 
     { (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
@@ -275,7 +282,7 @@ class DictState(
     }
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     val deserializers = nested.states.map(_.deserialize(codec))
 
     { (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
@@ -314,17 +321,17 @@ class GroupedAggregator(ktV: VirtualTypeWithReq, nestedAggs: Array[StagedAggrega
   val initOpTypes: Seq[Type] = Array(TVoid)
   val seqOpTypes: Seq[Type] = Array(ktV.t, TVoid)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     val Array(inits) = init
     state.init(cb, cb => cb += inits.asVoid())
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(key, seqs) = seq
     state.withContainer(cb, key, (cb) => cb += seqs.asVoid())
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
diff --git a/hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
index 22d63b43a7b..55647eb3bcf 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/ImputeTypeAggregator.scala
@@ -3,6 +3,7 @@ package is.hail.expr.ir.agg
 import is.hail.annotations.Region
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.types.{RPrimitive, VirtualTypeWithReq}
 import is.hail.types.physical.stypes.EmitType
@@ -10,7 +11,6 @@ import is.hail.types.physical.stypes.concrete.SStackStruct
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.{SBoolean, SBooleanValue}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 object ImputeTypeState {
   val resultVirtualType = TStruct(
@@ -168,20 +168,20 @@ class ImputeTypeAggregator() extends StagedAggregator {
 
   type State = ImputeTypeState
 
-  def resultEmitType = ImputeTypeState.resultEmitType
+  override def resultEmitType = ImputeTypeState.resultEmitType
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 0)
     state.initialize(cb)
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(s) = seq
 
     state.seqOp(cb, s)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -190,7 +190,8 @@ class ImputeTypeAggregator() extends StagedAggregator {
   ): Unit =
     state.combOp(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     val emitCodes = Array(
       state.getAnyNonMissing,
       state.getAllDefined,
diff --git a/hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
index 6f43d58ccb4..c6b4559ff09 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/LinearRegressionAggregator.scala
@@ -134,7 +134,7 @@ class LinearRegressionAggregator() extends StagedAggregator {
     cb += Region.storeInt(stateType.loadField(state.off, 2), k0)
   }
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     val Array(kt, k0t) = init
     kt.toI(cb)
       .consume(
@@ -254,7 +254,7 @@ class LinearRegressionAggregator() extends StagedAggregator {
     )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(y, x) = seq
     y.toI(cb)
       .consume(
@@ -321,7 +321,7 @@ class LinearRegressionAggregator() extends StagedAggregator {
     )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -330,7 +330,8 @@ class LinearRegressionAggregator() extends StagedAggregator {
   ): Unit =
     combOpF(state, other)(cb)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode = {
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode = {
     val resAddr = cb.newLocal[Long](
       "linear_regression_agg_res",
       Code.invokeScalaObject4[Region, Long, Long, Int, Long](
diff --git a/hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala
index c6162cb2ce7..58bacbdc7db 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/MonoidAggregator.scala
@@ -22,12 +22,12 @@ trait StagedMonoidSpec {
 class MonoidAggregator(monoid: StagedMonoidSpec) extends StagedAggregator {
   type State = PrimitiveRVAState
   val sType = SType.canonical(monoid.typ)
-  def resultEmitType = EmitType(sType, monoid.neutral.isDefined)
+  override def resultEmitType = EmitType(sType, monoid.neutral.isDefined)
 
   val initOpTypes: Seq[Type] = Array[Type]()
   val seqOpTypes: Seq[Type] = Array[Type](monoid.typ)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 0)
     val stateRequired = state.vtypes.head.r.required
     val ev = state.fields(0)
@@ -40,14 +40,14 @@ class MonoidAggregator(monoid: StagedMonoidSpec) extends StagedAggregator {
     }
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(elt) = seq
     val ev = state.fields(0)
     val update = cb.memoizeField(elt, "monoid_elt")
     combine(cb, ev, update)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -59,7 +59,8 @@ class MonoidAggregator(monoid: StagedMonoidSpec) extends StagedAggregator {
     combine(cb, ev1, ev2)
   }
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     state.fields(0).toI(cb)
 
   private def combine(
@@ -81,7 +82,7 @@ class MonoidAggregator(monoid: StagedMonoidSpec) extends StagedAggregator {
 
 class ComparisonMonoid(val typ: Type, val functionName: String) extends StagedMonoidSpec {
 
-  def neutral: Option[Value[_]] = None
+  override def neutral: Option[Value[_]] = None
 
   private def cmp[T](v1: Code[T], v2: Code[T])(implicit tct: ClassTag[T]): Code[T] =
     Code.invokeStatic2[Math, T, T, T](functionName, v1, v2)
@@ -89,7 +90,7 @@ class ComparisonMonoid(val typ: Type, val functionName: String) extends StagedMo
   private def nancmp[T](v1: Code[T], v2: Code[T])(implicit tct: ClassTag[T]): Code[T] =
     Code.invokeScalaObject2[T, T, T](UtilFunctions.getClass, "nan" + functionName, v1, v2)
 
-  def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
+  override def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
     case TInt32 => cb.memoize(cmp[Int](coerce(v1), coerce(v2)))
     case TInt64 => cb.memoize(cmp[Long](coerce(v1), coerce(v2)))
     case TFloat32 => cb.memoize(nancmp[Float](coerce(v1), coerce(v2)))
@@ -100,13 +101,13 @@ class ComparisonMonoid(val typ: Type, val functionName: String) extends StagedMo
 
 class SumMonoid(val typ: Type) extends StagedMonoidSpec {
 
-  def neutral: Option[Value[_]] = Some(typ match {
+  override def neutral: Option[Value[_]] = Some(typ match {
     case TInt64 => const(0L)
     case TFloat64 => const(0.0d)
     case _ => throw new UnsupportedOperationException(s"can't sum over type $typ")
   })
 
-  def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
+  override def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
     case TInt64 => cb.memoize(coerce[Long](v1) + coerce[Long](v2))
     case TFloat64 => cb.memoize(coerce[Double](v1) + coerce[Double](v2))
     case _ => throw new UnsupportedOperationException(s"can't sum over type $typ")
@@ -115,13 +116,13 @@ class SumMonoid(val typ: Type) extends StagedMonoidSpec {
 
 class ProductMonoid(val typ: Type) extends StagedMonoidSpec {
 
-  def neutral: Option[Value[_]] = Some(typ match {
+  override def neutral: Option[Value[_]] = Some(typ match {
     case TInt64 => const(1L)
     case TFloat64 => const(1.0d)
     case _ => throw new UnsupportedOperationException(s"can't product over type $typ")
   })
 
-  def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
+  override def apply(cb: EmitCodeBuilder, v1: Value[_], v2: Value[_]): Value[_] = typ match {
     case TInt64 => cb.memoize(coerce[Long](v1) * coerce[Long](v2))
     case TFloat64 => cb.memoize(coerce[Double](v1) * coerce[Double](v2))
     case _ => throw new UnsupportedOperationException(s"can't product over type $typ")
diff --git a/hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
index bae7d64d3b4..1f770cd7e3f 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/NDArrayMultiplyAddAggregator.scala
@@ -2,7 +2,9 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{CodeParamType, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.linalg.LinalgCodeUtils
 import is.hail.types.VirtualTypeWithReq
@@ -10,7 +12,6 @@ import is.hail.types.physical.PCanonicalNDArray
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.interfaces.{SNDArray, SNDArrayValue}
 import is.hail.types.virtual.Type
-import is.hail.utils.{valueToRichCodeRegion, FastSeq}
 
 class NDArrayMultiplyAddAggregator(ndVTyp: VirtualTypeWithReq) extends StagedAggregator {
   override type State = TypedRegionBackedAggState
diff --git a/hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala
index 7d403580a45..1e30c35b3d7 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/NDArraySumAggregator.scala
@@ -2,14 +2,15 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{CodeParamType, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.types.VirtualTypeWithReq
 import is.hail.types.physical.PCanonicalNDArray
 import is.hail.types.physical.stypes.{EmitType, SCode}
 import is.hail.types.physical.stypes.interfaces.SNDArrayValue
 import is.hail.types.virtual.Type
-import is.hail.utils._
 
 class NDArraySumAggregator(ndVTyp: VirtualTypeWithReq) extends StagedAggregator {
   override type State = TypedRegionBackedAggState
@@ -99,7 +100,8 @@ class NDArraySumAggregator(ndVTyp: VirtualTypeWithReq) extends StagedAggregator
     cb.invokeVoid(combOpMethod, cb.this_)
   }
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     state.get(cb).map(cb)(sv => sv.copyToRegion(cb, region, sv.st))
 }
 
diff --git a/hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
index 5f124f46210..74e6fee5320 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/PrevNonNullAggregator.scala
@@ -14,12 +14,12 @@ class PrevNonNullAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
   val initOpTypes: Seq[Type] = Array[Type]()
   val seqOpTypes: Seq[Type] = Array[Type](typ.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 0)
     state.storeMissing(cb)
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(elt: EmitCode) = seq
     elt.toI(cb)
       .consume(
@@ -29,7 +29,7 @@ class PrevNonNullAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
       )
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -43,6 +43,7 @@ class PrevNonNullAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
         sc => state.storeNonmissing(cb, sc),
       )
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     state.get(cb).map(cb)(sv => sv.copyToRegion(cb, region, sv.st))
 }
diff --git a/hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
index ecc38217718..25a6579fe07 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/ReservoirSampleAggregator.scala
@@ -2,7 +2,11 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitMethodBuilder, IEmitCode}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
 import is.hail.types.VirtualTypeWithReq
@@ -10,7 +14,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.virtual.{TInt32, Type}
-import is.hail.utils._
 
 class ReservoirSampleRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
     extends AggregatorState {
@@ -33,10 +36,10 @@ class ReservoirSampleRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuil
   private val garbageOffset: Code[Long] => Code[Long] = storageType.loadField(_, 2)
   private val builderStateOffset: Code[Long] => Code[Long] = storageType.loadField(_, 3)
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
     cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit = {
+  override def createState(cb: EmitCodeBuilder): Unit = {
     cb.assign(rand, Code.newInstance[java.util.Random]())
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
   }
@@ -70,14 +73,14 @@ class ReservoirSampleRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuil
     )
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       cb += ob.writeInt(maxSize)
       cb += ob.writeLong(seenSoFar)
       builder.serialize(codec)(cb, ob)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
       cb.assign(maxSize, ib.readInt())
       cb.assign(seenSoFar, ib.readLong())
@@ -245,7 +248,7 @@ class ReservoirSampleRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuil
       builder.loadElement(cb, idx).toI(cb)
     }
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     cb.assign(maxSize, Region.loadInt(maxSizeOffset(src)))
     cb.assign(seenSoFar, Region.loadLong(elementsSeenOffset(src)))
     cb.assign(garbage, Region.loadLong(garbageOffset(src)))
@@ -262,8 +265,11 @@ class ReservoirSampleAggregator(typ: VirtualTypeWithReq) extends StagedAggregato
   val initOpTypes: Seq[Type] = Array(TInt32)
   val seqOpTypes: Seq[Type] = Array(typ.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: ReservoirSampleRVAS, init: Array[EmitCode])
-    : Unit = {
+  override protected def _initOp(
+    cb: EmitCodeBuilder,
+    state: ReservoirSampleRVAS,
+    init: Array[EmitCode],
+  ): Unit = {
     assert(init.length == 1)
     val Array(sizeTriplet) = init
     sizeTriplet.toI(cb)
@@ -274,13 +280,16 @@ class ReservoirSampleAggregator(typ: VirtualTypeWithReq) extends StagedAggregato
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: ReservoirSampleRVAS, seq: Array[EmitCode])
-    : Unit = {
+  override protected def _seqOp(
+    cb: EmitCodeBuilder,
+    state: ReservoirSampleRVAS,
+    seq: Array[EmitCode],
+  ): Unit = {
     val Array(elt: EmitCode) = seq
     state.seqOp(cb, elt)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -288,7 +297,8 @@ class ReservoirSampleAggregator(typ: VirtualTypeWithReq) extends StagedAggregato
     other: ReservoirSampleRVAS,
   ): Unit = state.combine(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     // deepCopy is handled by state.resultArray
     IEmitCode.present(cb, state.resultArray(cb, region, resultPType))
 }
diff --git a/hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala b/hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala
index 05a10575a07..a9696a112e2 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/StagedArrayBuilder.scala
@@ -2,11 +2,11 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitValue}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer, TypedCodecSpec}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.SValue
-import is.hail.utils._
 
 object StagedArrayBuilder {
   val END_SERIALIZATION: Int = 0x12345678
diff --git a/hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala b/hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
index c79d98189f1..ecda9a24171 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/StagedBlockLinkedList.scala
@@ -2,13 +2,16 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.encoded._
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.SIndexablePointerValue
-import is.hail.utils._
 
 object StagedBlockLinkedList {
   val defaultBlockCap: Int = 64
diff --git a/hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala
index 00295f2efad..d362b8b203c 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/TakeAggregator.scala
@@ -2,6 +2,9 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
 import is.hail.expr.ir.{EmitClassBuilder, EmitCode, EmitCodeBuilder, IEmitCode}
 import is.hail.io.{BufferSpec, InputBuffer, OutputBuffer}
@@ -10,7 +13,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.virtual.{TInt32, Type}
-import is.hail.utils._
 
 class TakeRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
     extends AggregatorState {
@@ -25,9 +27,10 @@ class TakeRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
   private val maxSizeOffset: Code[Long] => Code[Long] = storageType.loadField(_, 0)
   private val builderStateOffset: Code[Long] => Code[Long] = storageType.loadField(_, 1)
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = cb += region.getNewRegion(regionSize)
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+    cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(region.isNull, cb.assign(r, Region.stagedCreate(regionSize, kb.pool())))
 
   override def load(
@@ -55,13 +58,13 @@ class TakeRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
     )
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       cb += ob.writeInt(maxSize)
       builder.serialize(codec)(cb, ob)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
       cb.assign(maxSize, ib.readInt())
       builder.deserialize(codec)(cb, ib)
@@ -97,7 +100,7 @@ class TakeRVAS(val eltType: VirtualTypeWithReq, val kb: EmitClassBuilder[_])
       builder.loadElement(cb, idx).toI(cb)
     }
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     cb.assign(maxSize, Region.loadInt(maxSizeOffset(src)))
     builder.copyFrom(cb, builderStateOffset(src))
   }
@@ -112,7 +115,7 @@ class TakeAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
   val initOpTypes: Seq[Type] = Array(TInt32)
   val seqOpTypes: Seq[Type] = Array(typ.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 1)
     val Array(sizeTriplet) = init
     sizeTriplet.toI(cb)
@@ -123,12 +126,12 @@ class TakeAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(elt: EmitCode) = seq
     state.seqOp(cb, elt)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -136,7 +139,8 @@ class TakeAggregator(typ: VirtualTypeWithReq) extends StagedAggregator {
     other: TakeRVAS,
   ): Unit = state.combine(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     // deepCopy is handled by state.resultArray
     IEmitCode.present(cb, state.resultArray(cb, region, resultPType))
 }
diff --git a/hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala b/hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala
index 3fa6237ba57..1248f11eb10 100644
--- a/hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala
+++ b/hail/hail/src/is/hail/expr/ir/agg/TakeByAggregator.scala
@@ -2,7 +2,12 @@ package is.hail.expr.ir.agg
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.{
+  codeToRichCodeRegion, valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer,
+  valueToRichCodeRegion,
+}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
   Ascending, EmitClassBuilder, EmitCode, EmitCodeBuilder, EmitValue, IEmitCode, ParamType, SortOrder,
 }
@@ -16,7 +21,6 @@ import is.hail.types.physical.stypes.concrete.{
 }
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.{TInt32, Type}
-import is.hail.utils._
 
 object TakeByRVAS {
   val END_SERIALIZATION: Int = 0x1324
@@ -100,9 +104,10 @@ class TakeByRVAS(
     }
   }
 
-  def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit = cb += region.getNewRegion(regionSize)
+  override def newState(cb: EmitCodeBuilder, off: Value[Long]): Unit =
+    cb += region.getNewRegion(regionSize)
 
-  def createState(cb: EmitCodeBuilder): Unit =
+  override def createState(cb: EmitCodeBuilder): Unit =
     cb.if_(
       region.isNull, {
         cb.assign(r, Region.stagedCreate(regionSize, kb.pool()))
@@ -193,7 +198,7 @@ class TakeByRVAS(
     })
   }
 
-  def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
+  override def copyFrom(cb: EmitCodeBuilder, src: Value[Long]): Unit = {
     maybeGCCode(
       cb,
       { cb =>
@@ -205,7 +210,7 @@ class TakeByRVAS(
     )({ cb => cb.assign(maxGarbage, Region.loadInt(storageType.fieldOffset(src, 4))) })
   }
 
-  def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
+  override def serialize(codec: BufferSpec): (EmitCodeBuilder, Value[OutputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ob: Value[OutputBuffer]) =>
       maybeGCCode(
         cb,
@@ -218,7 +223,7 @@ class TakeByRVAS(
       )(cb => cb += ob.writeInt(maxGarbage), runBefore = true)
   }
 
-  def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
+  override def deserialize(codec: BufferSpec): (EmitCodeBuilder, Value[InputBuffer]) => Unit = {
     (cb: EmitCodeBuilder, ib: Value[InputBuffer]) =>
       maybeGCCode(
         cb,
@@ -676,7 +681,7 @@ class TakeByAggregator(valueType: VirtualTypeWithReq, keyType: VirtualTypeWithRe
   val initOpTypes: Seq[Type] = Array(TInt32)
   val seqOpTypes: Seq[Type] = Array(valueType.t, keyType.t)
 
-  protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
+  override protected def _initOp(cb: EmitCodeBuilder, state: State, init: Array[EmitCode]): Unit = {
     assert(init.length == 1)
     val Array(sizeTriplet) = init
     sizeTriplet.toI(cb)
@@ -687,12 +692,12 @@ class TakeByAggregator(valueType: VirtualTypeWithReq, keyType: VirtualTypeWithRe
       )
   }
 
-  protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
+  override protected def _seqOp(cb: EmitCodeBuilder, state: State, seq: Array[EmitCode]): Unit = {
     val Array(value: EmitCode, key: EmitCode) = seq
     state.seqOp(cb, value, key)
   }
 
-  protected def _combOp(
+  override protected def _combOp(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     region: Value[Region],
@@ -700,7 +705,8 @@ class TakeByAggregator(valueType: VirtualTypeWithReq, keyType: VirtualTypeWithRe
     other: TakeByRVAS,
   ): Unit = state.combine(cb, other)
 
-  protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region]): IEmitCode =
+  override protected def _result(cb: EmitCodeBuilder, state: State, region: Value[Region])
+    : IEmitCode =
     // state.result does a deep copy
     IEmitCode.present(
       cb,
diff --git a/hail/hail/src/is/hail/expr/ir/analyses/RowCounts.scala b/hail/hail/src/is/hail/expr/ir/analyses/RowCounts.scala
index 2e483aa61b3..c065d7440de 100644
--- a/hail/hail/src/is/hail/expr/ir/analyses/RowCounts.scala
+++ b/hail/hail/src/is/hail/expr/ir/analyses/RowCounts.scala
@@ -1,7 +1,8 @@
 package is.hail.expr.ir.analyses
 
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichOption
 import is.hail.expr.ir._
-import is.hail.utils.{toRichOption, FastSeq}
 import is.hail.utils.PartitionCounts.{getHeadPCs, getTailPCs}
 
 object PartitionCounts {
diff --git a/hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala b/hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala
index 4e0f2db011b..27a138b4dae 100644
--- a/hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala
+++ b/hail/hail/src/is/hail/expr/ir/analyses/SemanticHash.scala
@@ -8,7 +8,8 @@ import is.hail.io.fs.FS
 import is.hail.io.vcf.MatrixVCFReader
 import is.hail.methods._
 import is.hail.types.virtual._
-import is.hail.utils.{toRichBoolean, Logging, TreeTraversal}
+import is.hail.utils.{Logging, TreeTraversal}
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.collection.mutable
 import scala.util.control.NonFatal
@@ -110,12 +111,6 @@ case object SemanticHash extends Logging {
         buffer ++= fname.getBytes
         tyArgs.foreach(buffer ++= EncodeTypename(_))
 
-      case ApplySeeded(fname, _, _, staticUID, retTy) =>
-        buffer ++=
-          fname.getBytes ++=
-          Bytes.fromLong(staticUID) ++=
-          EncodeTypename(retTy): Unit
-
       case ApplySpecial(fname, tyArgs, _, retTy, _) =>
         buffer ++= fname.getBytes
         tyArgs.foreach(buffer ++= EncodeTypename(_))
@@ -219,6 +214,9 @@ case object SemanticHash extends Logging {
       case RelationalRef(name, _) =>
         buffer ++= name.str.getBytes
 
+      case RNGSplitStatic(_, staticUid) =>
+        buffer ++= Bytes.fromLong(staticUid)
+
       case SelectFields(struct, names) =>
         val getFieldIndex = struct.typ.asInstanceOf[TStruct].fieldIdx
         names.map(getFieldIndex).foreach(buffer ++= Bytes.fromInt(_))
diff --git a/hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
index 657ca2a1a9a..7b3098c1e07 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/ApproxCDFFunctions.scala
@@ -2,13 +2,13 @@ package is.hail.expr.ir.functions
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{valueToCodeObject, Code, Value}
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.expr.ir.agg.{ApproxCDFStateManager, QuantilesAggregator}
 import is.hail.types.physical.stypes.concrete.SBaseStructPointer
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
 import is.hail.types.physical.stypes.primitives.SInt32Value
 import is.hail.types.virtual.TInt32
-import is.hail.utils.toRichIterable
 
 import org.apache.spark.sql.Row
 
@@ -51,7 +51,7 @@ object ApproxCDFFunctions extends RegistryFunctions {
     unwrapReturn(cb, r, SBaseStructPointer(statePType), row).asBaseStruct
   }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerSCode3(
       "approxCDFCombine",
       TInt32,
@@ -61,12 +61,12 @@ object ApproxCDFFunctions extends RegistryFunctions {
       (_, _, _, _) => SBaseStructPointer(statePType),
     ) {
       case (r, cb, _, k: SInt32Value, left: SBaseStructValue, right: SBaseStructValue, _) =>
-        val leftState = makeStateManager(cb, r.region, k.value, left)
-        val rightState = makeStateManager(cb, r.region, k.value, right)
+        val leftState = makeStateManager(cb, r, k.value, left)
+        val rightState = makeStateManager(cb, r, k.value, right)
 
         cb += leftState.invoke[ApproxCDFStateManager, Unit]("combOp", rightState)
 
-        fromStateManager(cb, r.region, leftState)
+        fromStateManager(cb, r, leftState)
     }
   }
 }
diff --git a/hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala
index 1123e18e4bb..3e72c2ccbef 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/ArrayFunctions.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir.functions
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.orderings.CodeOrdering
@@ -11,7 +12,6 @@ import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.{SBooleanValue, SFloat64, SInt32, SInt32Value}
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
-import is.hail.utils._
 
 object ArrayFunctions extends RegistryFunctions {
   val arrayOps: Array[(String, Type, Type, (IR, IR, Int) => IR)] =
@@ -120,7 +120,7 @@ object ArrayFunctions extends RegistryFunctions {
     foldIR(ToStream(a), one)((product, v) => ApplyBinaryPrimOp(Multiply(), product, v))
   }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerIR1("isEmpty", TArray(tv("T")), TBoolean)((_, a, _) => isEmpty(a))
 
     registerIR2("extend", TArray(tv("T")), TArray(tv("T")), TArray(tv("T")))((_, a, b, _) =>
@@ -342,7 +342,7 @@ object ArrayFunctions extends RegistryFunctions {
         )
         val pt = rt.pType.asInstanceOf[PCanonicalArray]
         val (push, finish) =
-          pt.constructFromIndicesUnsafe(cb, er.region, len.value, deepCopy = false)
+          pt.constructFromIndicesUnsafe(cb, er, len.value, deepCopy = false)
         indices.forEachDefined(cb) { case (cb, pos, idx: SInt32Value) =>
           cb.if_(
             idx.value < 0 || idx.value >= len.value,
diff --git a/hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala
index 6920d0b760a..aab47deda2e 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/CallFunctions.scala
@@ -12,7 +12,7 @@ import is.hail.variant._
 import scala.reflect.classTag
 
 object CallFunctions extends RegistryFunctions {
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerWrappedScalaFunction1("Call", TString, TCall, (rt: Type, st: SType) => SCanonicalCall)(
       Call.getClass,
       "parse",
diff --git a/hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala
index 5771280f4f1..fa42467c3d5 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/DictFunctions.scala
@@ -1,10 +1,10 @@
 package is.hail.expr.ir.functions
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.types
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object DictFunctions extends RegistryFunctions {
   def contains(dict: IR, key: IR) = {
@@ -49,7 +49,7 @@ object DictFunctions extends RegistryFunctions {
 
   val tdict = TDict(tv("key"), tv("value"))
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerIR1("isEmpty", tdict, TBoolean)((_, d, _) => ArrayFunctions.isEmpty(CastToArray(d)))
 
     registerIR2("contains", tdict, tv("key"), TBoolean)((_, a, b, _) => contains(a, b))
diff --git a/hail/hail/src/is/hail/expr/ir/functions/Functions.scala b/hail/hail/src/is/hail/expr/ir/functions/Functions.scala
index 287866330e0..9abb8e19eb4 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/Functions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/Functions.scala
@@ -2,10 +2,13 @@ package is.hail.expr.ir.functions
 
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.experimental.ExperimentalFunctions
 import is.hail.expr.ir._
-import is.hail.expr.ir.defs.{Apply, ApplyIR, ApplySeeded, ApplySpecial}
+import is.hail.expr.ir.defs.{Apply, ApplyIR, ApplySpecial}
 import is.hail.io.bgen.BGENFunctions
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SType, SValue}
@@ -184,18 +187,11 @@ object IRFunctionRegistry {
     }
   }
 
-  def lookupSeeded(name: String, staticUID: Long, returnType: Type, arguments: Seq[Type])
-    : Option[(Seq[IR], IR) => IR] =
-    lookupFunction(name, returnType, Array.empty[Type], TRNGState +: arguments)
-      .map { f => (irArguments: Seq[IR], rngState: IR) =>
-        ApplySeeded(name, irArguments.toFastSeq, rngState, staticUID, f.returnType.subst())
-      }
-
-  def lookupUnseeded(name: String, returnType: Type, arguments: Seq[Type])
+  def lookup(name: String, returnType: Type, arguments: Seq[Type])
     : Option[ConcreteIRFunctionImplementation] =
-    lookupUnseeded(name, returnType, Array.empty[Type], arguments)
+    lookup(name, returnType, Array.empty[Type], arguments)
 
-  def lookupUnseeded(
+  def lookup(
     name: String,
     returnType: Type,
     typeParameters: Seq[Type],
@@ -465,13 +461,13 @@ abstract class RegistryFunctions {
     calculateReturnType: (Type, Seq[SType]) => SType,
     typeParameters: Array[Type] = Array.empty,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, Seq[Type], SType, Array[SValue], Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, Seq[Type], SType, Array[SValue], Value[Int]) => SValue
   ): Unit = {
     IRFunctionRegistry.addJVMFunction(
       new UnseededMissingnessObliviousJVMFunction(name, typeParameters, valueParameterTypes,
         returnType, calculateReturnType) {
         override def apply(
-          r: EmitRegion,
+          r: Value[Region],
           cb: EmitCodeBuilder,
           returnSType: SType,
           typeParameters: Seq[Type],
@@ -490,13 +486,13 @@ abstract class RegistryFunctions {
     calculateReturnType: (Type, Seq[SType]) => SType,
     typeParameters: Array[Type] = Array.empty,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, SType, Array[Type], Array[SValue]) => Value[_]
+    impl: (Value[Region], EmitCodeBuilder, SType, Array[Type], Array[SValue]) => Value[_]
   ): Unit = {
     IRFunctionRegistry.addJVMFunction(
       new UnseededMissingnessObliviousJVMFunction(name, typeParameters, valueParameterTypes,
         returnType, calculateReturnType) {
         override def apply(
-          r: EmitRegion,
+          r: Value[Region],
           cb: EmitCodeBuilder,
           returnSType: SType,
           typeParameters: Seq[Type],
@@ -518,20 +514,21 @@ abstract class RegistryFunctions {
     calculateReturnType: (Type, Seq[EmitType]) => EmitType,
     typeParameters: Array[Type] = Array.empty,
   )(
-    impl: (EmitRegion, SType, Value[Int], Array[EmitCode]) => EmitCode
+    impl: (EmitMethodBuilder[_], Value[Region], SType, Value[Int], Array[EmitCode]) => EmitCode
   ): Unit = {
     IRFunctionRegistry.addJVMFunction(
       new UnseededMissingnessAwareJVMFunction(name, typeParameters, valueParameterTypes, returnType,
         calculateReturnType) {
         override def apply(
-          r: EmitRegion,
+          mb: EmitMethodBuilder[_],
+          region: Value[Region],
           rpt: SType,
           typeParameters: Seq[Type],
           errorID: Value[Int],
           args: EmitCode*
         ): EmitCode = {
           assert(unify(typeParameters, args.map(_.st.virtualType), rpt.virtualType))
-          impl(r, rpt, errorID, args.toArray)
+          impl(mb, region, rpt, errorID, args.toArray)
         }
       }
     )
@@ -566,13 +563,14 @@ abstract class RegistryFunctions {
           res
         }
         override def apply(
-          r: EmitRegion,
+          mb: EmitMethodBuilder[_],
+          region: Value[Region],
           rpt: SType,
           typeParameters: Seq[Type],
           errorID: Value[Int],
           args: EmitCode*
         ): EmitCode =
-          EmitCode.fromI(r.mb)(cb => apply(cb, r.region, rpt, typeParameters, errorID, args: _*))
+          EmitCode.fromI(mb)(cb => apply(cb, region, rpt, typeParameters, errorID, args: _*))
       }
     )
   }
@@ -646,16 +644,12 @@ abstract class RegistryFunctions {
     registerSCode(name, valueParameterTypes, returnType, calculateReturnType) {
       case (r, cb, _, rt, args, _) =>
         val cts = valueParameterTypes.map(ct(_).runtimeClass)
-        try
-          unwrapReturn(
-            cb,
-            r.region,
-            rt,
-            Code.invokeScalaObject(cls, method, cts, args.map(a => wrap(cb, r.region, a).get))(
-              ct(returnType)
-            ),
+        try {
+          val ret = Code.invokeScalaObject(cls, method, cts, args.map(a => wrap(cb, r, a).get))(
+            ct(returnType)
           )
-        catch {
+          unwrapReturn(cb, r, rt, ret)
+        } catch {
           case e: Throwable =>
             throw new RuntimeException(s"error while registering function $name", e)
         }
@@ -754,7 +748,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, SType, SValue, Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, SType, SValue, Value[Int]) => SValue
   ): Unit =
     registerSCode(name, Array(mt1), rt, unwrappedApply(pt)) {
       case (r, cb, _, rt, Array(a1), errorID) => impl(r, cb, rt, a1, errorID)
@@ -767,7 +761,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, Seq[Type], SType, SValue, Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, Seq[Type], SType, SValue, Value[Int]) => SValue
   ): Unit =
     registerSCode(name, Array(mt1), rt, unwrappedApply(pt), typeParameters = typeParams) {
       case (r, cb, typeParams, rt, Array(a1), errorID) => impl(r, cb, typeParams, rt, a1, errorID)
@@ -780,7 +774,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, SType, SValue, SValue, Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, SType, SValue, SValue, Value[Int]) => SValue
   ): Unit =
     registerSCode(name, Array(mt1, mt2), rt, unwrappedApply(pt)) {
       case (r, cb, _, rt, Array(a1, a2), errorID) => impl(r, cb, rt, a1, a2, errorID)
@@ -794,7 +788,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, Seq[Type], SType, SValue, SValue, Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, Seq[Type], SType, SValue, SValue, Value[Int]) => SValue
   ): Unit =
     registerSCode(name, Array(mt1, mt2), rt, unwrappedApply(pt), typeParameters = typeParams) {
       case (r, cb, typeParams, rt, Array(a1, a2), errorID) =>
@@ -809,7 +803,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType, SType, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, SType, SValue, SValue, SValue, Value[Int]) => SValue
+    impl: (Value[Region], EmitCodeBuilder, SType, SValue, SValue, SValue, Value[Int]) => SValue
   ): Unit =
     registerSCode(name, Array(mt1, mt2, mt3), rt, unwrappedApply(pt)) {
       case (r, cb, _, rt, Array(a1, a2, a3), errorID) => impl(r, cb, rt, a1, a2, a3, errorID)
@@ -825,7 +819,7 @@ abstract class RegistryFunctions {
     pt: (Type, SType, SType, SType) => SType,
   )(
     impl: (
-      EmitRegion,
+      Value[Region],
       EmitCodeBuilder,
       Seq[Type],
       SType,
@@ -849,7 +843,16 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType, SType, SType, SType) => SType,
   )(
-    impl: (EmitRegion, EmitCodeBuilder, SType, SValue, SValue, SValue, SValue, Value[Int]) => SValue
+    impl: (
+      Value[Region],
+      EmitCodeBuilder,
+      SType,
+      SValue,
+      SValue,
+      SValue,
+      SValue,
+      Value[Int],
+    ) => SValue
   ): Unit =
     registerSCode(name, Array(mt1, mt2, mt3, mt4), rt, unwrappedApply(pt)) {
       case (r, cb, _, rt, Array(a1, a2, a3, a4), errorID) =>
@@ -867,7 +870,7 @@ abstract class RegistryFunctions {
     pt: (Type, SType, SType, SType, SType) => SType,
   )(
     impl: (
-      EmitRegion,
+      Value[Region],
       EmitCodeBuilder,
       Seq[Type],
       SType,
@@ -894,7 +897,7 @@ abstract class RegistryFunctions {
     pt: (Type, SType, SType, SType, SType, SType) => SType,
   )(
     impl: (
-      EmitRegion,
+      Value[Region],
       EmitCodeBuilder,
       SType,
       SValue,
@@ -922,7 +925,7 @@ abstract class RegistryFunctions {
     pt: (Type, SType, SType, SType, SType, SType, SType) => SType,
   )(
     impl: (
-      EmitRegion,
+      Value[Region],
       EmitCodeBuilder,
       SType,
       SValue,
@@ -952,7 +955,7 @@ abstract class RegistryFunctions {
     pt: (Type, SType, SType, SType, SType, SType, SType, SType) => SType,
   )(
     impl: (
-      EmitRegion,
+      Value[Region],
       EmitCodeBuilder,
       SType,
       SValue,
@@ -976,7 +979,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType) => SType,
   )(
-    impl: (EmitCodeBuilder, EmitRegion, SType, SValue) => Value[_]
+    impl: (EmitCodeBuilder, Value[Region], SType, SValue) => Value[_]
   ): Unit =
     registerCode(name, Array(mt1), rt, unwrappedApply(pt)) {
       case (r, cb, rt, _, Array(a1)) => impl(cb, r, rt, a1)
@@ -989,7 +992,7 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, SType, SType) => SType,
   )(
-    impl: (EmitCodeBuilder, EmitRegion, SType, SValue, SValue) => Value[_]
+    impl: (EmitCodeBuilder, Value[Region], SType, SValue, SValue) => Value[_]
   ): Unit =
     registerCode(name, Array(mt1, mt2), rt, unwrappedApply(pt)) {
       case (r, cb, rt, _, Array(a1, a2)) => impl(cb, r, rt, a1, a2)
@@ -1133,10 +1136,10 @@ abstract class RegistryFunctions {
     rt: Type,
     pt: (Type, EmitType, EmitType) => EmitType,
   )(
-    impl: (EmitRegion, SType, Value[Int], EmitCode, EmitCode) => EmitCode
+    impl: (EmitMethodBuilder[_], Value[Region], SType, Value[Int], EmitCode, EmitCode) => EmitCode
   ): Unit =
     registerEmitCode(name, Array(mt1, mt2), rt, unwrappedApply(pt)) {
-      case (r, rt, errorID, Array(a1, a2)) => impl(r, rt, errorID, a1, a2)
+      case (mb, r, rt, errorID, Array(a1, a2)) => impl(mb, r, rt, errorID, a1, a2)
     }
 
   def registerIR1(
@@ -1206,7 +1209,8 @@ sealed abstract class JVMFunction {
   def computeReturnEmitType(returnType: Type, valueParameterTypes: Seq[EmitType]): EmitType
 
   def apply(
-    mb: EmitRegion,
+    mb: EmitMethodBuilder[_],
+    region: Value[Region],
     returnType: SType,
     typeParameters: Seq[Type],
     errorID: Value[Int],
@@ -1261,7 +1265,7 @@ abstract class UnseededMissingnessObliviousJVMFunction(
     )
 
   def apply(
-    r: EmitRegion,
+    r: Value[Region],
     cb: EmitCodeBuilder,
     returnSType: SType,
     typeParameters: Seq[Type],
@@ -1269,21 +1273,22 @@ abstract class UnseededMissingnessObliviousJVMFunction(
     args: SValue*
   ): SValue
 
-  def apply(
-    r: EmitRegion,
+  override def apply(
+    mb: EmitMethodBuilder[_],
+    region: Value[Region],
     returnType: SType,
     typeParameters: Seq[Type],
     errorID: Value[Int],
     args: EmitCode*
   ): EmitCode =
-    EmitCode.fromI(r.mb)(cb =>
+    EmitCode.fromI(mb)(cb =>
       IEmitCode.multiMapEmitCodes(cb, args.toFastSeq) { args =>
-        apply(r, cb, returnType, typeParameters, errorID, args: _*)
+        apply(region, cb, returnType, typeParameters, errorID, args: _*)
       }
     )
 
   def applyI(
-    r: EmitRegion,
+    r: Value[Region],
     cb: EmitCodeBuilder,
     returnType: SType,
     typeParameters: Seq[Type],
@@ -1305,12 +1310,12 @@ abstract class UnseededMissingnessObliviousJVMFunction(
     )
     methodbuilder.emitSCode(cb =>
       apply(
-        EmitRegion.default(methodbuilder),
+        methodbuilder.getCodeParam[Region](1),
         cb,
         rpt,
         typeParameters,
         methodbuilder.getCodeParam[Int](2),
-        (0 until args.length).map(i => methodbuilder.getSCodeParam(i + 3)): _*
+        args.indices.map(i => methodbuilder.getSCodeParam(i + 3)): _*
       )
     )
     methodbuilder
diff --git a/hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala
index 272686ac2f7..48f5e114c85 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/GenotypeFunctions.scala
@@ -9,7 +9,7 @@ import is.hail.types.virtual.{TArray, TFloat64, TInt32, Type}
 
 object GenotypeFunctions extends RegistryFunctions {
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerSCode1("gqFromPL", TArray(tv("N", "int32")), TInt32, (_: Type, _: SType) => SInt32) {
       case (_, cb, _, pl: SIndexableValue, errorID) =>
         val m = cb.newLocal[Int]("m", 99)
diff --git a/hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala
index bcf277ce170..600cd1dd14a 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/IntervalFunctions.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir.functions
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.orderings.CodeOrdering
 import is.hail.types.physical._
@@ -9,7 +10,6 @@ import is.hail.types.physical.stypes.concrete.{SIntervalPointer, SStackStruct, S
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.{SBoolean, SBooleanValue, SInt32}
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object IntervalFunctions extends RegistryFunctions {
 
@@ -306,7 +306,7 @@ object IntervalFunctions extends RegistryFunctions {
     BinarySearch.equalRange(cb, array, compare, ltNeedle, gtNeedle, 0, array.loadLength)
   }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerIEmitCode4(
       "Interval",
       tv("T"),
diff --git a/hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala
index 7f607977aa7..464adc54000 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/LocusFunctions.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.functions
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitMethodBuilder, _}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SType}
@@ -118,7 +119,7 @@ object LocusFunctions extends RegistryFunctions {
         )))
     }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     val locusClass = Locus.getClass
 
     registerSCode1(
@@ -160,8 +161,8 @@ object LocusFunctions extends RegistryFunctions {
         SCanonicalLocusPointer(PCanonicalLocus(tl.asInstanceOf[TLocus].rg)),
     ) {
       case (
-            r: EmitRegion,
-            cb: EmitCodeBuilder,
+            r,
+            cb,
             rt: SCanonicalLocusPointer,
             inputLocus: SLocusValue,
             basePairsToAdd: SInt32Value,
@@ -182,7 +183,7 @@ object LocusFunctions extends RegistryFunctions {
             )),
           ),
         )
-        rt.pType.constructFromContigAndPosition(cb, r.region, contig, newPos)
+        rt.pType.constructFromContigAndPosition(cb, r, contig, newPos)
     }
 
     registerSCode2(
@@ -215,10 +216,10 @@ object LocusFunctions extends RegistryFunctions {
             VariantMethods.getClass,
             "minRep",
             locus.getLocusObj(cb),
-            Code.checkcast[IndexedSeq[String]](svalueToJavaValue(cb, r.region, alleles)),
+            Code.checkcast[IndexedSeq[String]](svalueToJavaValue(cb, r, alleles)),
           )
 
-        emitVariant(cb, r.region, variantTuple, rt)
+        emitVariant(cb, r, variantTuple, rt)
     }
 
     registerSCode2(
@@ -234,8 +235,8 @@ object LocusFunctions extends RegistryFunctions {
         ).sType,
     ) {
       case (
-            r: EmitRegion,
-            cb: EmitCodeBuilder,
+            r,
+            cb,
             SBaseStructPointer(rt: PCanonicalTuple),
             grouped: SIndexableValue,
             radiusVal: SFloat64Value,
@@ -276,7 +277,7 @@ object LocusFunctions extends RegistryFunctions {
         ): IEmitCode = {
 
           val (pushElement, finish) =
-            arrayType.constructFromFunctions(cb, r.region, totalLen, deepCopy = false)
+            arrayType.constructFromFunctions(cb, r, totalLen, deepCopy = false)
           val offset = cb.newLocal[Int]("locuswindows_offset", 0)
 
           val lastCoord = cb.newLocal[Double]("locuswindows_coord")
@@ -350,7 +351,7 @@ object LocusFunctions extends RegistryFunctions {
 
         rt.constructFromFields(
           cb,
-          r.region,
+          r,
           FastSeq[EmitCode](
             EmitCode.fromI(cb.emb)(cb =>
               addIdxWithCondition(cb) { case (cb, i, idx, coords) =>
@@ -389,12 +390,12 @@ object LocusFunctions extends RegistryFunctions {
         val slocus = str.loadString(cb)
         emitLocus(
           cb,
-          r.region,
+          r,
           Code.invokeScalaObject2[String, ReferenceGenome, Locus](
             locusClass,
             "parse",
             slocus,
-            rgCode(r.mb, rt.rg),
+            rgCode(cb.emb, rt.rg),
           ),
           rt,
         )
@@ -409,14 +410,14 @@ object LocusFunctions extends RegistryFunctions {
         PCanonicalLocus(returnType.asInstanceOf[TLocus].rg).sType,
     ) {
       case (r, cb, SCanonicalLocusPointer(rt: PCanonicalLocus), contig, pos, _) =>
-        cb += rgCode(r.mb, rt.rg).invoke[String, Int, Unit](
+        cb += rgCode(cb.emb, rt.rg).invoke[String, Int, Unit](
           "checkLocus",
           contig.asString.loadString(cb),
           pos.asInt.value,
         )
         rt.constructFromContigAndPosition(
           cb,
-          r.region,
+          r,
           contig.asString.loadString(cb),
           pos.asInt.value,
         )
@@ -443,9 +444,9 @@ object LocusFunctions extends RegistryFunctions {
             VariantMethods.getClass,
             "parse",
             svar,
-            rgCode(r.mb, plocus.rg),
+            rgCode(cb.emb, plocus.rg),
           )
-        emitVariant(cb, r.region, variant, rt)
+        emitVariant(cb, r, variant, rt)
     }
 
     registerIEmitCode2(
@@ -586,21 +587,24 @@ object LocusFunctions extends RegistryFunctions {
       case (r, cb, SCanonicalLocusPointer(rt: PCanonicalLocus), globalPos, _) =>
         val locus = cb.newLocal[Locus](
           "global_pos_locus",
-          rgCode(r.mb, rt.rg).invoke[Long, Locus]("globalPosToLocus", globalPos.asLong.value),
+          rgCode(cb.emb, rt.rg).invoke[Long, Locus]("globalPosToLocus", globalPos.asLong.value),
         )
         rt.constructFromContigAndPosition(
           cb,
-          r.region,
+          r,
           locus.invoke[String]("contig"),
           locus.invoke[Int]("position"),
         )
     }
 
     registerSCode1("locusToGlobalPos", tlocus("T"), TInt64, (_: Type, _: SType) => SInt64) {
-      case (r, cb, _, locus: SLocusValue, _) =>
+      case (_, cb, _, locus: SLocusValue, _) =>
         val locusObject = locus.getLocusObj(cb)
         val globalPos =
-          cb.memoize(rgCode(r.mb, locus.st.rg).invoke[Locus, Long]("locusToGlobalPos", locusObject))
+          cb.memoize(rgCode(cb.emb, locus.st.rg).invoke[Locus, Long](
+            "locusToGlobalPos",
+            locusObject,
+          ))
         primitive(globalPos)
     }
 
diff --git a/hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala
index 517b50e431b..8c21df16eec 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/MathFunctions.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir.functions
 
 import is.hail.asm4s.Code
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitValue
 import is.hail.expr.ir.defs.{Cast, ErrorIDs}
 import is.hail.stats._
@@ -111,7 +112,7 @@ object MathFunctions extends RegistryFunctions {
 
   val mathPackageClass: Class[_] = Class.forName("scala.math.package$")
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     val thisClass = getClass
     val statsPackageClass = Class.forName("is.hail.stats.package$")
     val jMathClass = classOf[java.lang.Math]
@@ -341,9 +342,9 @@ object MathFunctions extends RegistryFunctions {
             statsPackageClass,
             "pgenchisq",
             x.value,
-            Code.checkcast[IndexedSeq[Double]](svalueToJavaValue(cb, r.region, w)),
-            Code.checkcast[IndexedSeq[Int]](svalueToJavaValue(cb, r.region, k)),
-            Code.checkcast[IndexedSeq[Double]](svalueToJavaValue(cb, r.region, lam)),
+            Code.checkcast[IndexedSeq[Double]](svalueToJavaValue(cb, r, w)),
+            Code.checkcast[IndexedSeq[Int]](svalueToJavaValue(cb, r, k)),
+            Code.checkcast[IndexedSeq[Double]](svalueToJavaValue(cb, r, lam)),
             sigma.value,
             maxIterations.value,
             minAccuracy.value,
@@ -352,7 +353,7 @@ object MathFunctions extends RegistryFunctions {
 
         DaviesAlgorithm.pType.constructFromFields(
           cb,
-          r.region,
+          r,
           FastSeq(
             EmitValue.present(primitive(cb.memoize(res.invoke[Double]("value")))),
             EmitValue.present(primitive(cb.memoize(res.invoke[Int]("nIterations")))),
@@ -439,7 +440,7 @@ object MathFunctions extends RegistryFunctions {
 
       fetStruct.constructFromFields(
         cb,
-        r.region,
+        r,
         FastSeq(
           EmitValue.present(primitive(cb.memoize(res(0)))),
           EmitValue.present(primitive(cb.memoize(res(1)))),
@@ -473,7 +474,7 @@ object MathFunctions extends RegistryFunctions {
 
       chisqStruct.constructFromFields(
         cb,
-        r.region,
+        r,
         FastSeq(
           EmitValue.present(primitive(cb.memoize(res(0)))),
           EmitValue.present(primitive(cb.memoize(res(1)))),
@@ -518,7 +519,7 @@ object MathFunctions extends RegistryFunctions {
 
         chisqStruct.constructFromFields(
           cb,
-          r.region,
+          r,
           FastSeq(
             EmitValue.present(primitive(cb.memoize(res(0)))),
             EmitValue.present(primitive(cb.memoize(res(1)))),
@@ -560,7 +561,7 @@ object MathFunctions extends RegistryFunctions {
 
         hweStruct.constructFromFields(
           cb,
-          r.region,
+          r,
           FastSeq(
             EmitValue.present(primitive(cb.memoize(res(0)))),
             EmitValue.present(primitive(cb.memoize(res(1)))),
diff --git a/hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala b/hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
index 72b9574b67c..e7594fbd48b 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/MatrixWriteBlockMatrix.scala
@@ -7,7 +7,7 @@ import is.hail.utils._
 
 import java.io.DataOutputStream
 
-import org.json4s.jackson
+import org.json4s.{jackson, DefaultFormats}
 
 object MatrixWriteBlockMatrix extends Logging {
   def apply(
@@ -51,7 +51,7 @@ object MatrixWriteBlockMatrix extends Logging {
 
     // write metadata
     using(new DataOutputStream(fs.create(path + BlockMatrix.metadataRelativePath))) { os =>
-      implicit val formats = defaultJSONFormats
+      implicit val formats = DefaultFormats
       jackson.Serialization.write(
         BlockMatrixMetadata(
           blockSize,
diff --git a/hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala
index 46a159154ef..c6608115720 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/NDArrayFunctions.scala
@@ -212,9 +212,9 @@ object NDArrayFunctions extends RegistryFunctions {
       TNDArray(TFloat64, Nat(2)),
       (t, p1, p2) => PCanonicalNDArray(PFloat64Required, 2, true).sType,
     ) {
-      case (er, cb, SNDArrayPointer(pt), apc, bpc, errorID) =>
+      case (r, cb, SNDArrayPointer(pt), apc, bpc, errorID) =>
         val (resPCode, info) =
-          linear_solve(apc.asNDArray, bpc.asNDArray, pt, cb, er.region, errorID)
+          linear_solve(apc.asNDArray, bpc.asNDArray, pt, cb, r, errorID)
         cb.if_(
           info cne 0,
           cb._fatalWithError(
@@ -287,14 +287,14 @@ object NDArrayFunctions extends RegistryFunctions {
       TNDArray(TFloat64, Nat(2)),
       (t, p1, p2, p3) => PCanonicalNDArray(PFloat64Required, 2, true).sType,
     ) {
-      case (er, cb, SNDArrayPointer(pt), apc, bpc, lower, errorID) =>
+      case (r, cb, SNDArrayPointer(pt), apc, bpc, lower, errorID) =>
         val (resPCode, info) = linear_triangular_solve(
           apc.asNDArray,
           bpc.asNDArray,
           lower.asBoolean,
           pt,
           cb,
-          er.region,
+          r,
           errorID,
         )
         cb.if_(
@@ -317,7 +317,7 @@ object NDArrayFunctions extends RegistryFunctions {
       (_, _, _, _) => PCanonicalNDArray(PFloat64Required, 2, true).sType,
     ) {
       case (
-            er,
+            r,
             cb,
             rst: SNDArrayPointer,
             block: SNDArrayValue,
@@ -325,7 +325,7 @@ object NDArrayFunctions extends RegistryFunctions {
             upper: SInt64Value,
             _,
           ) =>
-        val newBlock = rst.coerceOrCopy(cb, er.region, block, deepCopy = false).asInstanceOf[
+        val newBlock = rst.coerceOrCopy(cb, r, block, deepCopy = false).asInstanceOf[
           SNDArrayPointerValue
         ]
         val IndexedSeq(nRows, nCols) = newBlock.shapes
@@ -351,13 +351,11 @@ object NDArrayFunctions extends RegistryFunctions {
                 cb.assign(j, j + 1L)
               },
               // block(i to i, 0 until j) := 0.0
-              newBlock.slice(cb, i, (null, j)).coiterateMutate(cb, er.region) { _ =>
-                primitive(0.0d)
-              },
+              newBlock.slice(cb, i, (null, j)).coiterateMutate(cb, r)(_ => primitive(0.0d)),
             )
 
             // block(iRight until nRows, ::) := 0.0
-            newBlock.slice(cb, (iRight, null), ColonIndex).coiterateMutate(cb, er.region) { _ =>
+            newBlock.slice(cb, (iRight, null), ColonIndex).coiterateMutate(cb, r) { _ =>
               primitive(0.0d)
             }
           },
@@ -369,7 +367,7 @@ object NDArrayFunctions extends RegistryFunctions {
             cb.assign(iRight, (nCols.get - upper.value).min(nRows.get))
 
             // block(0 util iLeft, ::) := 0.0
-            newBlock.slice(cb, (null, iLeft), ColonIndex).coiterateMutate(cb, er.region) { _ =>
+            newBlock.slice(cb, (null, iLeft), ColonIndex).coiterateMutate(cb, r) { _ =>
               primitive(0.0d)
             }
 
@@ -383,9 +381,7 @@ object NDArrayFunctions extends RegistryFunctions {
                 cb.assign(j, j + 1)
               },
               // block(i to i, j to nCols) := 0.0
-              newBlock.slice(cb, i, (j, null)).coiterateMutate(cb, er.region) { _ =>
-                primitive(0.0d)
-              },
+              newBlock.slice(cb, i, (j, null)).coiterateMutate(cb, r)(_ => primitive(0.0d)),
             )
           },
         )
@@ -402,7 +398,7 @@ object NDArrayFunctions extends RegistryFunctions {
       (_, _, _, _) => PCanonicalNDArray(PFloat64Required, 2, true).sType,
     ) {
       case (
-            er,
+            r,
             cb,
             rst: SNDArrayPointer,
             block: SNDArrayValue,
@@ -410,7 +406,7 @@ object NDArrayFunctions extends RegistryFunctions {
             stops: SIndexableValue,
             _,
           ) =>
-        val newBlock = rst.coerceOrCopy(cb, er.region, block, deepCopy = false).asInstanceOf[
+        val newBlock = rst.coerceOrCopy(cb, r, block, deepCopy = false).asInstanceOf[
           SNDArrayPointerValue
         ]
         val row = cb.newLocal[Long]("rowIdx")
@@ -421,12 +417,8 @@ object NDArrayFunctions extends RegistryFunctions {
           cb.assign(row, row + 1L), {
             val start = starts.loadElement(cb, row.toI).getOrAssert(cb).asInt64.value
             val stop = stops.loadElement(cb, row.toI).getOrAssert(cb).asInt64.value
-            newBlock.slice(cb, row, (null, start)).coiterateMutate(cb, er.region) { _ =>
-              primitive(0.0d)
-            }
-            newBlock.slice(cb, row, (stop, null)).coiterateMutate(cb, er.region) { _ =>
-              primitive(0.0d)
-            }
+            newBlock.slice(cb, row, (null, start)).coiterateMutate(cb, r)(_ => primitive(0.0d))
+            newBlock.slice(cb, row, (stop, null)).coiterateMutate(cb, r)(_ => primitive(0.0d))
           },
         )
 
diff --git a/hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala
index a5036a39b90..301a5da7782 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/RandomSeededFunctions.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir.functions
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical.{PCanonicalArray, PCanonicalNDArray, PFloat64, PInt32}
@@ -9,66 +10,6 @@ import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SNDArrayPointe
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
-
-import net.sourceforge.jdistlib.{Beta, Gamma, HyperGeometric, Poisson}
-import net.sourceforge.jdistlib.rng.MersenneTwister
-
-class IRRandomness(seed: Long) {
-
-  /* org.apache.commons has no way to statically sample from distributions without creating objects
-   * :( */
-  private[this] val random = new MersenneTwister()
-  private[this] val poisState = Poisson.create_random_state()
-
-  // FIXME: these are just combined with some large primes, so probably should be fixed up
-  private[this] def hash(pidx: Int): Long =
-    seed ^ java.lang.Math.floorMod(pidx * 11399L, 2147483647L)
-
-  def reset(partitionIdx: Int): Unit = {
-    val combinedSeed = hash(partitionIdx)
-    random.setSeed(combinedSeed)
-  }
-
-  def runif(min: Double, max: Double): Double = min + (max - min) * random.nextDouble()
-
-  def rint32(n: Int): Int = random.nextInt(n)
-
-  def rint64(): Long = random.nextLong()
-
-  def rint64(n: Long): Long = random.nextLong(n)
-
-  def rcoin(p: Double): Boolean = random.nextDouble() < p
-
-  def rpois(lambda: Double): Double = Poisson.random(lambda, random, poisState)
-
-  def rnorm(mean: Double, sd: Double): Double = mean + sd * random.nextGaussian()
-
-  def rnorm(): Double = rnorm(0, 1)
-
-  def rbeta(a: Double, b: Double): Double = Beta.random(a, b, random)
-
-  def rgamma(shape: Double, scale: Double): Double = Gamma.random(shape, scale, random)
-
-  def rhyper(numSuccessStates: Double, numFailureStates: Double, numToDraw: Double): Double =
-    HyperGeometric.random(numSuccessStates, numFailureStates, numToDraw, random)
-
-  def rcat(prob: Array[Double]): Int = {
-    var i = 0
-    var sum = 0.0
-    while (i < prob.length) {
-      sum += prob(i)
-      i += 1
-    }
-    var draw = random.nextDouble() * sum
-    i = 0
-    while (draw > prob(i)) {
-      draw -= prob(i)
-      i += 1
-    }
-    i
-  }
-}
 
 object RandomSeededFunctions extends RegistryFunctions {
 
@@ -111,7 +52,7 @@ object RandomSeededFunctions extends RegistryFunctions {
     )
   }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerSCode3(
       "rand_unif",
       TRNGState,
@@ -156,11 +97,11 @@ object RandomSeededFunctions extends RegistryFunctions {
         val result = rt.pType.constructUninitialized(
           FastSeq(SizeValueDyn(nRows.value), SizeValueDyn(nCols.value)),
           cb,
-          r.region,
+          r,
         )
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
-        result.coiterateMutate(cb, r.region) { _ =>
+        result.coiterateMutate(cb, r) { _ =>
           primitive(cb.memoize(rng.invoke[Double, Double, Double](
             "runif",
             min.asDouble.value,
@@ -179,7 +120,7 @@ object RandomSeededFunctions extends RegistryFunctions {
         case (_: Type, _: SType, _: SType) => SInt32
       },
     ) { case (_, cb, _, rngState: SRNGStateValue, n: SInt32Value, _) =>
-      val rng = cb.emb.getThreefryRNG()
+      val rng = cb.emb.threefryRandomEngine
       rngState.copyIntoEngine(cb, rng)
       primitive(cb.memoize(rng.invoke[Int, Int]("nextInt", n.value)))
     }
@@ -193,7 +134,7 @@ object RandomSeededFunctions extends RegistryFunctions {
         case (_: Type, _: SType, _: SType) => SInt64
       },
     ) { case (_, cb, _, rngState: SRNGStateValue, n: SInt64Value, _) =>
-      val rng = cb.emb.getThreefryRNG()
+      val rng = cb.emb.threefryRandomEngine
       rngState.copyIntoEngine(cb, rng)
       primitive(cb.memoize(rng.invoke[Long, Long]("nextLong", n.value)))
     }
@@ -236,11 +177,11 @@ object RandomSeededFunctions extends RegistryFunctions {
         val result = rt.pType.constructUninitialized(
           FastSeq(SizeValueDyn(nRows.value), SizeValueDyn(nCols.value)),
           cb,
-          r.region,
+          r,
         )
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
-        result.coiterateMutate(cb, r.region) { _ =>
+        result.coiterateMutate(cb, r) { _ =>
           primitive(cb.memoize(rng.invoke[Double, Double, Double](
             "rnorm",
             mean.asDouble.value,
@@ -261,7 +202,7 @@ object RandomSeededFunctions extends RegistryFunctions {
       },
     ) {
       case (_, cb, _, rngState: SRNGStateValue, mean: SFloat64Value, sd: SFloat64Value, _) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
         primitive(cb.memoize(rng.invoke[Double, Double, Double]("rnorm", mean.value, sd.value)))
     }
@@ -288,7 +229,7 @@ object RandomSeededFunctions extends RegistryFunctions {
         case (_: Type, _: SType, _: SType) => SFloat64
       },
     ) { case (_, cb, _, rngState: SRNGStateValue, lambda: SFloat64Value, _) =>
-      val rng = cb.emb.getThreefryRNG()
+      val rng = cb.emb.threefryRandomEngine
       rngState.copyIntoEngine(cb, rng)
       primitive(cb.memoize(rng.invoke[Double, Double]("rpois", lambda.value)))
     }
@@ -312,9 +253,9 @@ object RandomSeededFunctions extends RegistryFunctions {
             lambda: SFloat64Value,
             _,
           ) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
-        rt.constructFromElements(cb, r.region, n.value, deepCopy = false) { case (cb, _) =>
+        rt.constructFromElements(cb, r, n.value, deepCopy = false) { case (cb, _) =>
           IEmitCode.present(
             cb,
             primitive(cb.memoize(rng.invoke[Double, Double]("rpois", lambda.value))),
@@ -332,7 +273,7 @@ object RandomSeededFunctions extends RegistryFunctions {
         case (_: Type, _: SType, _: SType, _: SType) => SFloat64
       },
     ) { case (_, cb, _, rngState: SRNGStateValue, a: SFloat64Value, b: SFloat64Value, _) =>
-      val rng = cb.emb.getThreefryRNG()
+      val rng = cb.emb.threefryRandomEngine
       rngState.copyIntoEngine(cb, rng)
       primitive(cb.memoize(rng.invoke[Double, Double, Double]("rbeta", a.value, b.value)))
     }
@@ -360,7 +301,7 @@ object RandomSeededFunctions extends RegistryFunctions {
             max: SFloat64Value,
             _,
           ) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
         val value = cb.newLocal[Double](
           "value",
@@ -384,7 +325,7 @@ object RandomSeededFunctions extends RegistryFunctions {
       },
     ) {
       case (_, cb, _, rngState: SRNGStateValue, a: SFloat64Value, scale: SFloat64Value, _) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
         primitive(cb.memoize(rng.invoke[Double, Double, Double]("rgamma", a.value, scale.value)))
     }
@@ -410,7 +351,7 @@ object RandomSeededFunctions extends RegistryFunctions {
             nSample: SInt32Value,
             _,
           ) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
         val nBad = popSize.value - nGood.value
         primitive(cb.memoize(rng.invoke[Double, Double, Double, Double](
@@ -433,10 +374,10 @@ object RandomSeededFunctions extends RegistryFunctions {
       },
     ) {
       case (r, cb, _, rngState: SRNGStateValue, colors: SIndexableValue, nSample: SInt32Value, _) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
         val (push, finish) = PCanonicalArray(PInt32(required = true))
-          .constructFromFunctions(cb, r.region, colors.loadLength, deepCopy = false)
+          .constructFromFunctions(cb, r, colors.loadLength, deepCopy = false)
         cb.if_(
           colors.hasMissingValues(cb),
           cb._fatal("rand_multi_hyper: colors may not contain missing values"),
@@ -521,7 +462,7 @@ object RandomSeededFunctions extends RegistryFunctions {
             partitionCounts: SIndexableValue,
             _,
           ) =>
-        val rng = cb.emb.getThreefryRNG()
+        val rng = cb.emb.threefryRandomEngine
         rngState.copyIntoEngine(cb, rng)
 
         val totalNumberOfRecords = cb.newLocal[Int]("scnspp_total_number_of_records", 0)
@@ -556,7 +497,7 @@ object RandomSeededFunctions extends RegistryFunctions {
         val arrayRt = rt.asInstanceOf[SIndexablePointer]
         val (push, finish) = arrayRt.pType.asInstanceOf[PCanonicalArray].constructFromFunctions(
           cb,
-          r.region,
+          r,
           resultSize,
           false,
         )
diff --git a/hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
index b51016e90d2..7fda87413fc 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/ReferenceGenomeFunctions.scala
@@ -14,7 +14,7 @@ object ReferenceGenomeFunctions extends RegistryFunctions {
   def rgCode(mb: EmitMethodBuilder[_], rg: String): Code[ReferenceGenome] =
     mb.getReferenceGenome(rg)
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerSCode1t(
       "isValidContig",
       Array(LocusFunctions.tlocus("R")),
@@ -22,12 +22,12 @@ object ReferenceGenomeFunctions extends RegistryFunctions {
       TBoolean,
       (_: Type, _: SType) => SBoolean,
     ) {
-      case (r, cb, Seq(tlocus: TLocus), _, contig, _) =>
+      case (_, cb, Seq(tlocus: TLocus), _, contig, _) =>
         val scontig = contig.asString.loadString(cb)
-        primitive(cb.memoize(rgCode(r.mb, tlocus.asInstanceOf[TLocus].rg).invoke[String, Boolean](
-          "isValidContig",
-          scontig,
-        )))
+        primitive(cb.memoize(
+          rgCode(cb.emb, tlocus.rg)
+            .invoke[String, Boolean]("isValidContig", scontig)
+        ))
     }
 
     registerSCode2t(
@@ -38,9 +38,9 @@ object ReferenceGenomeFunctions extends RegistryFunctions {
       TBoolean,
       (_: Type, _: SType, _: SType) => SBoolean,
     ) {
-      case (r, cb, Seq(tlocus: TLocus), _, contig, pos, _) =>
+      case (_, cb, Seq(tlocus: TLocus), _, contig, pos, _) =>
         val scontig = contig.asString.loadString(cb)
-        primitive(cb.memoize(rgCode(r.mb, tlocus.rg).invoke[String, Int, Boolean](
+        primitive(cb.memoize(rgCode(cb.emb, tlocus.rg).invoke[String, Int, Boolean](
           "isValidLocus",
           scontig,
           pos.asInt.value,
@@ -61,7 +61,7 @@ object ReferenceGenomeFunctions extends RegistryFunctions {
         val scontig = contig.asString.loadString(cb)
         unwrapReturn(
           cb,
-          r.region,
+          r,
           st,
           rgCode(cb.emb, typeParam.rg).invoke[String, Int, Int, Int, String](
             "getSequence",
@@ -80,9 +80,12 @@ object ReferenceGenomeFunctions extends RegistryFunctions {
       TInt32,
       (_: Type, _: SType) => SInt32,
     ) {
-      case (r, cb, Seq(tlocus: TLocus), _, contig, _) =>
+      case (_, cb, Seq(tlocus: TLocus), _, contig, _) =>
         val scontig = contig.asString.loadString(cb)
-        primitive(cb.memoize(rgCode(r.mb, tlocus.rg).invoke[String, Int]("contigLength", scontig)))
+        primitive(cb.memoize(rgCode(cb.emb, tlocus.rg).invoke[String, Int](
+          "contigLength",
+          scontig,
+        )))
     }
 
     registerIR(
diff --git a/hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala
index 03a7070783b..b4e19fc6dae 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/RelationalFunctions.scala
@@ -48,7 +48,7 @@ case class WrappedMatrixToTableFunction(
     function.typ(mType) // MatrixType RVDTypes will go away
   }
 
-  def execute(ctx: ExecuteContext, tv: TableValue): TableValue =
+  override def execute(ctx: ExecuteContext, tv: TableValue): TableValue =
     function.execute(ctx, tv.toMatrixValue(colKey, colsFieldName, entriesFieldName))
 
   override def preservesPartitionCounts: Boolean = function.preservesPartitionCounts
@@ -82,13 +82,13 @@ case class WrappedMatrixToValueFunction(
   colKey: IndexedSeq[String],
 ) extends TableToValueFunction {
 
-  def typ(childType: TableType): Type =
+  override def typ(childType: TableType): Type =
     function.typ(MatrixType.fromTableType(childType, colsFieldName, entriesFieldName, colKey))
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit =
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit =
     function.unionRequiredness(childType, resultType)
 
-  def execute(ctx: ExecuteContext, tv: TableValue): Any =
+  override def execute(ctx: ExecuteContext, tv: TableValue): Any =
     function.execute(ctx, tv.toMatrixValue(colKey, colsFieldName, entriesFieldName))
 }
 
diff --git a/hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala
index 9446ddc7ede..1dd27728296 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/SetFunctions.scala
@@ -1,9 +1,9 @@
 package is.hail.expr.ir.functions
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object SetFunctions extends RegistryFunctions {
   def contains(set: IR, elem: IR) = {
@@ -20,7 +20,7 @@ object SetFunctions extends RegistryFunctions {
     )
   }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerIR1("toSet", TArray(tv("T")), TSet(tv("T")))((_, a, _) => ToSet(ToStream(a)))
 
     registerIR1("isEmpty", TSet(tv("T")), TBoolean) { (_, s, _) =>
diff --git a/hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala
index a8fd0eb010e..029b8ce6e06 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/StringFunctions.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.functions
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.{FastSeq, StringArrayBuilder}
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
@@ -26,11 +27,7 @@ import org.json4s.JValue
 import org.json4s.jackson.JsonMethods
 
 object StringFunctions extends RegistryFunctions {
-  def reverse(s: String): String = {
-    val sb = new StringBuilder
-    sb.append(s)
-    sb.reverseContents().result()
-  }
+  def reverse(s: String): String = s.reverse
 
   def upper(s: String): String = s.toUpperCase
 
@@ -287,11 +284,11 @@ object StringFunctions extends RegistryFunctions {
       .parse(timeStr)
       .getLong(ChronoField.INSTANT_SECONDS)
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     val thisClass = getClass
 
     registerSCode1("length", TString, TInt32, (_: Type, _: SType) => SInt32) {
-      case (_: EmitRegion, cb, _, s: SStringValue, _) =>
+      case (_, cb, _, s: SStringValue, _) =>
         primitive(cb.memoize(s.loadString(cb).invoke[Int]("length")))
     }
 
@@ -303,7 +300,7 @@ object StringFunctions extends RegistryFunctions {
       TString,
       (_: Type, _: SType, _: SType, _: SType) => SJavaString,
     ) {
-      case (_: EmitRegion, cb, st: SJavaString.type, s, start, end, _) =>
+      case (_, cb, st: SJavaString.type, s, start, end, _) =>
         val str = s.asString.loadString(cb).invoke[Int, Int, String](
           "substring",
           start.asInt.value,
@@ -358,7 +355,7 @@ object StringFunctions extends RegistryFunctions {
 
     registerSCode1("str", tv("T"), TString, (_: Type, _: SType) => SJavaString) {
       case (r, cb, st: SJavaString.type, a, _) =>
-        val annotation = svalueToJavaValue(cb, r.region, a)
+        val annotation = svalueToJavaValue(cb, r, a)
         val str = cb.emb.getType(a.st.virtualType).invoke[Any, String]("str", annotation)
         st.construct(cb, str)
     }
@@ -719,8 +716,8 @@ object StringFunctions extends RegistryFunctions {
       {
         case (_: Type, _: EmitType, _: EmitType) => EmitType(SInt32, false)
       },
-    ) { case (r: EmitRegion, _, _, e1: EmitCode, e2: EmitCode) =>
-      EmitCode.fromI(r.mb) { cb =>
+    ) { case (mb, _, _, _, e1, e2) =>
+      EmitCode.fromI(mb) { cb =>
         e1.toI(cb).flatMap(cb) { case sc1: SStringValue =>
           e2.toI(cb).flatMap(cb) { case sc2: SStringValue =>
             val n = cb.newLocal("hamming_n", 0)
@@ -789,7 +786,7 @@ object StringFunctions extends RegistryFunctions {
       TTuple(tv("T")),
       (rType: Type, _: Seq[SType]) => SType.canonical(rType),
       typeParameters = Array(tv("T")),
-    ) { case (er, cb, _, resultType, Array(s: SStringValue), _) =>
+    ) { case (r, cb, _, resultType, Array(s: SStringValue), _) =>
       val warnCtx = cb.emb.genFieldThisRef[mutable.HashSet[String]]("parse_json_context")
       cb.if_(warnCtx.load().isNull, cb.assign(warnCtx, Code.newInstance[mutable.HashSet[String]]()))
 
@@ -797,11 +794,11 @@ object StringFunctions extends RegistryFunctions {
         JSONAnnotationImpex.getClass,
         "irImportAnnotation",
         s.loadString(cb),
-        er.mb.ecb.getType(resultType.virtualType.asInstanceOf[TTuple].types(0)),
+        cb.emb.ecb.getType(resultType.virtualType.asInstanceOf[TTuple].types(0)),
         warnCtx,
       )
 
-      unwrapReturn(cb, er.region, resultType, row)
+      unwrapReturn(cb, r, resultType, row)
     }
   }
 }
diff --git a/hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala b/hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
index 9c502d21ccc..2320317c5c9 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/TableCalculateNewPartitions.scala
@@ -1,18 +1,19 @@
 package is.hail.expr.ir.functions
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TableValue
 import is.hail.rvd.RVD
 import is.hail.types
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case class TableCalculateNewPartitions(
   nPartitions: Int
 ) extends TableToValueFunction {
-  def typ(childType: TableType): Type = TArray(TInterval(childType.keyType))
+  override def typ(childType: TableType): Type = TArray(TInterval(childType.keyType))
 
-  def unionRequiredness(childType: types.RTable, resultType: types.TypeWithRequiredness): Unit = {
+  override def unionRequiredness(childType: types.RTable, resultType: types.TypeWithRequiredness)
+    : Unit = {
     val rinterval = types.tcoerce[types.RInterval](
       types.tcoerce[types.RIterable](resultType).elementType
     )
@@ -24,7 +25,7 @@ case class TableCalculateNewPartitions(
     }
   }
 
-  def execute(ctx: ExecuteContext, tv: TableValue): Any = {
+  override def execute(ctx: ExecuteContext, tv: TableValue): Any = {
     val rvd = tv.rvd
     if (rvd.typ.key.isEmpty)
       FastSeq()
diff --git a/hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala b/hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala
index b089f9deb42..62cf5a3f0c7 100644
--- a/hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala
+++ b/hail/hail/src/is/hail/expr/ir/functions/UtilFunctions.scala
@@ -13,6 +13,7 @@ import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives._
 import is.hail.types.virtual._
 import is.hail.utils._
+import is.hail.utils.implicits.toRichString
 
 import scala.reflect.ClassTag
 
@@ -201,7 +202,7 @@ object UtilFunctions extends RegistryFunctions {
         )
     }
 
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     val thisClass = getClass
 
     registerSCode4(
@@ -215,14 +216,14 @@ object UtilFunctions extends RegistryFunctions {
         case (_: Type, _: SType, _: SType, _: SType, _: SType) => SBoolean
       },
     ) {
-      case (er, cb, _, l, r, tol, abs, _) =>
+      case (region, cb, _, l, r, tol, abs, _) =>
         assert(
           l.st.virtualType == r.st.virtualType,
           s"\n  lt=${l.st.virtualType}\n  rt=${r.st.virtualType}",
         )
-        val lb = svalueToJavaValue(cb, er.region, l)
-        val rb = svalueToJavaValue(cb, er.region, r)
-        primitive(cb.memoize(er.mb.getType(l.st.virtualType).invoke[
+        val lb = svalueToJavaValue(cb, region, l)
+        val rb = svalueToJavaValue(cb, region, r)
+        primitive(cb.memoize(cb.emb.getType(l.st.virtualType).invoke[
           Any,
           Any,
           Double,
@@ -517,7 +518,7 @@ object UtilFunctions extends RegistryFunctions {
       (_: Type, _: SType, _: SType) => SJavaString,
     ) {
       case (r, cb, st: SJavaString.type, format, args, _) =>
-        val javaObjArgs = Code.checkcast[Row](svalueToJavaValue(cb, r.region, args))
+        val javaObjArgs = Code.checkcast[Row](svalueToJavaValue(cb, r, args))
         val formatted = Code.invokeScalaObject2[String, Row, String](
           thisClass,
           "format",
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/ExecuteRelational.scala b/hail/hail/src/is/hail/expr/ir/lowering/ExecuteRelational.scala
index 2d3b1283b56..1cf14dadcbe 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/ExecuteRelational.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/ExecuteRelational.scala
@@ -6,8 +6,7 @@ import is.hail.expr.ir._
 import is.hail.expr.ir.analyses.PartitionCounts
 import is.hail.rvd.{RVD, RVDPartitioner}
 import is.hail.types.physical.PStruct
-import is.hail.utils.fatal
-import is.hail.utils.prettyPrint.ArrayOfByteArrayInputStream
+import is.hail.utils.{fatal, ArrayOfByteArrayInputStream}
 
 object ExecuteRelational {
   def apply(ctx: ExecuteContext, ir: TableIR): TableExecuteIntermediate =
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/Invariant.scala b/hail/hail/src/is/hail/expr/ir/lowering/Invariant.scala
index 8f05bd49c11..94c8d9fa0f6 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/Invariant.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/Invariant.scala
@@ -5,8 +5,8 @@ import is.hail.expr.ir.{
   BaseIR, BlockMatrixIR, Compilable, Emittable, IR, IRTraversal, MatrixIR, RelationalLetMatrixTable,
   RelationalLetTable, TableIR, TableKeyBy, TableKeyByAndAggregate, TableOrderBy,
 }
-import is.hail.expr.ir.defs.{ApplyIR, RelationalLet, RelationalRef}
-import is.hail.utils.toRichPredicate
+import is.hail.expr.ir.defs.{ApplyIR, LiftMeOut, RelationalLet, RelationalRef}
+import is.hail.utils.implicits.toRichPredicate
 
 abstract class Invariant(implicit E: sourcecode.Enclosing) extends (BaseIR => Boolean) {
   final def verify(ctx: ExecuteContext, ir: BaseIR): Unit =
@@ -46,6 +46,9 @@ object Invariant {
       case _ => true
     }
 
+  lazy val NoLiftMeOuts: Invariant =
+    Invariant(!_.isInstanceOf[LiftMeOut])
+
   lazy val NoApplyIR: Invariant =
     Invariant(!_.isInstanceOf[ApplyIR])
 
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
index 5f9361c2184..ef8484d284e 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LowerAndExecuteShuffles.scala
@@ -1,12 +1,12 @@
 package is.hail.expr.ir.lowering
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{Requiredness, _}
 import is.hail.expr.ir.agg.{Extract, PhysicalAggSig, TakeStateSig}
 import is.hail.expr.ir.defs._
 import is.hail.types._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object LowerAndExecuteShuffles {
 
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
index 644d3fc3226..8121e6bf4a2 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LowerBlockMatrixIR.scala
@@ -1,6 +1,9 @@
 package is.hail.expr.ir.lowering
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.{AnyRefArrayBuilder, FastSeq, LongArrayBuilder}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterator
 import is.hail.expr.Nat
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
@@ -9,8 +12,6 @@ import is.hail.linalg.MatrixSparsity
 import is.hail.rvd.RVDPartitioner
 import is.hail.types.{tcoerce, TypeWithRequiredness}
 import is.hail.types.virtual._
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import org.apache.spark.sql.Row
 
@@ -83,19 +84,19 @@ abstract class BlockMatrixStage(val broadcastVals: IndexedSeq[Ref], val ctxType:
     val outer = this
     val newCtxType = TStruct("old" -> ctxType, "new" -> newTyp)
     new BlockMatrixStage(broadcastVals, newCtxType) {
-      def blockContext(idx: (Int, Int)): IR =
+      override def blockContext(idx: (Int, Int)): IR =
         makestruct("old" -> outer.blockContext(idx), "new" -> newCtx(idx))
 
-      def blockBody(ctxRef: Ref): IR = bindIR(GetField(ctxRef, "old"))(outer.blockBody)
+      override def blockBody(ctxRef: Ref): IR = bindIR(GetField(ctxRef, "old"))(outer.blockBody)
     }
   }
 
   def mapBody(f: (IR, IR) => IR): BlockMatrixStage = {
     val outer = this
     new BlockMatrixStage(broadcastVals, outer.ctxType) {
-      def blockContext(idx: (Int, Int)): IR = outer.blockContext(idx)
+      override def blockContext(idx: (Int, Int)): IR = outer.blockContext(idx)
 
-      def blockBody(ctxRef: Ref): IR = f(ctxRef, outer.blockBody(ctxRef))
+      override def blockBody(ctxRef: Ref): IR = f(ctxRef, outer.blockBody(ctxRef))
     }
   }
 
@@ -107,7 +108,7 @@ abstract class BlockMatrixStage(val broadcastVals: IndexedSeq[Ref], val ctxType:
     val outer = this
     val ctxType = TArray(TArray(TTuple(TTuple(TInt64, TInt64), outer.ctxType)))
     new BlockMatrixStage(outer.broadcastVals, ctxType) {
-      def blockContext(idx: (Int, Int)): IR = {
+      override def blockContext(idx: (Int, Int)): IR = {
         val i = idx._1
         val j = idx._2
         MakeArray(rowBlocks(i).map { ii =>
@@ -125,7 +126,7 @@ abstract class BlockMatrixStage(val broadcastVals: IndexedSeq[Ref], val ctxType:
         }: _*)
       }
 
-      def blockBody(ctxRef: Ref): IR = {
+      override def blockBody(ctxRef: Ref): IR = {
         NDArrayConcat(
           ToArray(mapIR(ToStream(ctxRef)) { ctxRows =>
             NDArrayConcat(
@@ -401,7 +402,7 @@ case class DenseContexts(sparsity: MatrixSparsity.Dense, dynamic: DynamicDenseCo
     DenseContexts(ib, sparsity, newContexts)
   }
 
-  def withNewSparsity(ib: IRBuilder, newSparsity: MatrixSparsity): BMSContexts = {
+  override def withNewSparsity(ib: IRBuilder, newSparsity: MatrixSparsity): BMSContexts = {
     require(newSparsity.nRows == sparsity.nRows && newSparsity.nCols == sparsity.nCols)
     newSparsity match {
       case sparse: MatrixSparsity.Sparse =>
@@ -413,7 +414,7 @@ case class DenseContexts(sparsity: MatrixSparsity.Dense, dynamic: DynamicDenseCo
     }
   }
 
-  def groupedByCol(ib: IRBuilder): DenseContexts = {
+  override def groupedByCol(ib: IRBuilder): DenseContexts = {
     val groupedContexts = ToArray(mapIR(rangeIR(nCols)) { col =>
       sliceArrayIR(contexts, col * nRows, (col + 1) * nRows)
     })
@@ -476,7 +477,7 @@ case class DenseContexts(sparsity: MatrixSparsity.Dense, dynamic: DynamicDenseCo
     DenseContexts(ib, MatrixSparsity.Dense(rowDeps.length, colDeps.length), newContexts)
   }
 
-  def collect(makeBlock: (Ref, Ref, Ref) => IR): IR = {
+  override def collect(makeBlock: (Ref, Ref, Ref) => IR): IR = {
     NDArrayConcat(
       ToArray(mapIR(rangeIR(nCols)) { j =>
         val colBlocks = mapIR(rangeIR(nRows)) { i =>
@@ -518,7 +519,7 @@ case class SparseContexts(
   override def map(ib: IRBuilder)(f: (IR, IR, IR, IR) => IR): SparseContexts =
     new SparseContexts(sparsity, dynamic.map(ib)(f))
 
-  def withNewSparsity(ib: IRBuilder, newSparsity: MatrixSparsity): BMSContexts = {
+  override def withNewSparsity(ib: IRBuilder, newSparsity: MatrixSparsity): BMSContexts = {
     require(newSparsity.nRows == sparsity.nRows && newSparsity.nCols == sparsity.nCols)
     newSparsity match {
       case sparse: MatrixSparsity.Sparse =>
@@ -1220,8 +1221,8 @@ object LowerBlockMatrixIR {
           val n = GetTupleElement(ctx, 1)
           val i = GetTupleElement(ctx, 2)
           val f = if (gaussian) "rand_norm_nd" else "rand_unif_nd"
-          val rngState = RNGSplit(RNGStateLiteral(), Cast(i, TInt64))
-          invokeSeeded(f, staticUID, TNDArray(TFloat64, Nat(2)), rngState, m, n, F64(0.0), F64(1.0))
+          val rngState = RNGSplit(RNGSplitStatic(RNGStateLiteral(), staticUID), Cast(i, TInt64))
+          invoke(f, TNDArray(TFloat64, Nat(2)), rngState, m, n, F64(0.0), F64(1.0))
         }
 
         BlockMatrixStage2(FastSeq(), x.typ, contexts, bodyIR)
@@ -1474,7 +1475,7 @@ object LowerBlockMatrixIR {
         val right = lower(rightIR)
         val newCtxType = TArray(TTuple(left.ctxType, right.ctxType))
         new BlockMatrixStage(left.broadcastVals ++ right.broadcastVals, newCtxType) {
-          def blockContext(idx: (Int, Int)): IR = {
+          override def blockContext(idx: (Int, Int)): IR = {
             val (i, j) = idx
             MakeArray(
               Array.tabulate[Option[IR]](leftIR.typ.nColBlocks) { k =>
@@ -1489,7 +1490,7 @@ object LowerBlockMatrixIR {
             )
           }
 
-          def blockBody(ctxRef: Ref): IR = {
+          override def blockBody(ctxRef: Ref): IR = {
             val tupleNDArrayStream = ToStream(ctxRef)
             val streamElementName = freshName()
             val streamElementRef =
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala
index 92330bd8e1a..52441b8fc7e 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LowerDistributedSort.scala
@@ -3,19 +3,20 @@ package is.hail.expr.ir.lowering
 import is.hail.annotations.{Annotation, ExtendedOrdering, Region, SafeRow}
 import is.hail.asm4s.{classInfo, AsmFunction1RegionLong, LongInfo}
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs._
-import is.hail.expr.ir.functions.{ArrayFunctions, IRRandomness, UtilFunctions}
+import is.hail.expr.ir.functions.{ArrayFunctions, UtilFunctions}
 import is.hail.io.{BufferSpec, TypedCodecSpec}
 import is.hail.rvd.RVDPartitioner
+import is.hail.sparkextras.implicits.toRichRow
 import is.hail.types.{tcoerce, RTable, VirtualTypeWithReq}
 import is.hail.types.physical.{PArray, PStruct}
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable.ArrayBuffer
 import scala.reflect.ClassTag
@@ -102,15 +103,17 @@ object LowerDistributedSort extends Logging {
 
     override def isDistinctlyKeyed: Boolean = false // FIXME: No default value
 
-    def rowRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+    override def rowRequiredness(ctx: ExecuteContext, requestedType: TableType)
+      : VirtualTypeWithReq =
       VirtualTypeWithReq.subset(requestedType.rowType, rt.rowType)
 
-    def globalRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+    override def globalRequiredness(ctx: ExecuteContext, requestedType: TableType)
+      : VirtualTypeWithReq =
       VirtualTypeWithReq.subset(requestedType.globalType, rt.globalType)
 
     override def toJValue: JValue = JString("LocalSortReader")
 
-    def renderShort(): String = "LocalSortReader"
+    override def renderShort(): String = "LocalSortReader"
 
     override def defaultRender(): String = "LocalSortReader"
 
@@ -165,7 +168,6 @@ object LowerDistributedSort extends Logging {
   ): TableReader = {
 
     val oversamplingNum = 3
-    val seed = 7L
     val maxBranchingFactor = ctx.getFlag("shuffle_max_branch_factor").toInt
     val defaultBranchingFactor = if (inputStage.numPartitions < maxBranchingFactor) {
       Math.max(2, inputStage.numPartitions)
@@ -243,7 +245,7 @@ object LowerDistributedSort extends Logging {
     )
 
     var i = 0
-    val rand = new IRRandomness(seed)
+    val rand = ThreefryRandomEngine()
 
     /* Loop state keeps track of three things. largeSegments are too big to sort locally so have to
      * broken up.
@@ -783,7 +785,7 @@ object LowerDistributedSort extends Logging {
   }
 
   def howManySamplesPerPartition(
-    rand: IRRandomness,
+    rand: ThreefryRandomEngine,
     totalNumberOfRecords: Long,
     initialNumSamplesToSelect: Int,
     partitionCounts: IndexedSeq[Long],
@@ -982,15 +984,16 @@ case class DistributionSortReader(
 
   override def isDistinctlyKeyed: Boolean = false // FIXME: No default value
 
-  def rowRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+  override def rowRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
     VirtualTypeWithReq.subset(requestedType.rowType, rt.rowType)
 
-  def globalRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+  override def globalRequiredness(ctx: ExecuteContext, requestedType: TableType)
+    : VirtualTypeWithReq =
     VirtualTypeWithReq.subset(requestedType.globalType, rt.globalType)
 
   override def toJValue: JValue = JString("DistributionSortReader")
 
-  def renderShort(): String = "DistributionSortReader"
+  override def renderShort(): String = "DistributionSortReader"
 
   override def defaultRender(): String = "DistributionSortReader"
 
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala
index 2d68697bf5d..74a453278dc 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIR.scala
@@ -1,6 +1,8 @@
 package is.hail.expr.ir.lowering
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{agg, TableNativeWriter, _}
 import is.hail.expr.ir.agg.AggExecuteContextExtensions
 import is.hail.expr.ir.analyses.PartitionCounts
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
index 23cb87ba06a..69985bba295 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LowerTableIRHelpers.scala
@@ -1,11 +1,11 @@
 package is.hail.expr.ir.lowering
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.types.RTable
 import is.hail.types.virtual.TStruct
-import is.hail.utils.FastSeq
 
 import scala.collection.compat._
 
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala b/hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala
index c238e529b00..5d78857576c 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/LoweringPass.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir.lowering
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.agg.Extract
 import is.hail.expr.ir.analyses.SemanticHash
@@ -8,7 +9,7 @@ import is.hail.expr.ir.defs.{
   ApplyIR, Begin, Let, RunAgg, RunAggScan, StreamAgg, StreamAggScan, StreamFor,
 }
 import is.hail.expr.ir.lowering.Invariant._
-import is.hail.utils._
+import is.hail.utils.implicits.toRichPredicate
 
 final class IrMetadata() {
   private[this] var hashCounter: Int = 0
@@ -61,7 +62,7 @@ case object LowerMatrixToTablePass extends LoweringPass {
   val after: Invariant = NoMatrixIR
   val context: String = "LowerMatrixToTable"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = ir match {
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = ir match {
     case x: IR => LowerMatrixIR(ctx, x)
     case x: TableIR => LowerMatrixIR(ctx, x)
     case x: MatrixIR => LowerMatrixIR(ctx, x)
@@ -71,10 +72,10 @@ case object LowerMatrixToTablePass extends LoweringPass {
 
 case object LiftRelationalValuesToRelationalLets extends LoweringPass {
   val before: Invariant = NoMatrixIR
-  val after: Invariant = NoMatrixIR
+  val after: Invariant = NoMatrixIR and NoLiftMeOuts
   val context: String = "LiftRelationalValuesToRelationalLets"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = LiftRelationalValues(ir)
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = LiftRelationalValues(ir)
 }
 
 case object LegacyInterpretNonCompilablePass extends LoweringPass {
@@ -82,7 +83,8 @@ case object LegacyInterpretNonCompilablePass extends LoweringPass {
   val after: Invariant = NoMatrixIR and NoRelationalLets and CompilableValueIRs
   val context: String = "InterpretNonCompilable"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = LowerOrInterpretNonCompilable(ctx, ir)
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
+    LowerOrInterpretNonCompilable(ctx, ir)
 }
 
 case object LowerOrInterpretNonCompilablePass extends LoweringPass {
@@ -90,7 +92,8 @@ case object LowerOrInterpretNonCompilablePass extends LoweringPass {
   val after: Invariant = CompilableIR
   val context: String = "LowerOrInterpretNonCompilable"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = LowerOrInterpretNonCompilable(ctx, ir)
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
+    LowerOrInterpretNonCompilable(ctx, ir)
 }
 
 case class LowerToDistributedArrayPass(t: DArrayLowering.Type) extends LoweringPass {
@@ -98,7 +101,8 @@ case class LowerToDistributedArrayPass(t: DArrayLowering.Type) extends LoweringP
   val after: Invariant = CompilableIR
   val context: String = "LowerToDistributedArray"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR = LowerToCDA(ir.asInstanceOf[IR], t, ctx)
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
+    LowerToCDA(ir.asInstanceOf[IR], t, ctx)
 }
 
 case object InlineApplyIR extends LoweringPass {
@@ -123,7 +127,7 @@ case object LowerArrayAggsToRunAggsPass extends LoweringPass {
   val after: Invariant = EmittableIR
   val context: String = "LowerArrayAggsToRunAggs"
 
-  def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
+  override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
     ctx.time {
       val x = ir.noSharing(ctx)
       val r = Requiredness(x, ctx)
@@ -172,8 +176,8 @@ case object LowerArrayAggsToRunAggsPass extends LoweringPass {
 }
 
 case class EvalRelationalLetsPass(passesBelow: LoweringPipeline) extends LoweringPass {
-  val before: Invariant = NoMatrixIR
-  val after: Invariant = NoMatrixIR and NoRelationalLets
+  val before: Invariant = NoMatrixIR and NoLiftMeOuts
+  val after: Invariant = before and NoRelationalLets
   val context: String = "EvalRelationalLets"
 
   override def transform(ctx: ExecuteContext, ir: BaseIR): BaseIR =
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala b/hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala
index 0dc13ec6598..a82ed3a4cf7 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/RVDToTableStage.scala
@@ -4,6 +4,7 @@ import is.hail.annotations.{BroadcastRow, Region, RegionValue}
 import is.hail.asm4s._
 import is.hail.backend.{BroadcastValue, ExecuteContext}
 import is.hail.backend.spark.{AnonymousDependency, SparkTaskContext}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs.{
@@ -17,7 +18,6 @@ import is.hail.types.{RTable, VirtualTypeWithReq}
 import is.hail.types.physical.{PArray, PStruct}
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
 import is.hail.types.virtual.{TStruct, TableType}
-import is.hail.utils.FastSeq
 
 import java.io.{ByteArrayInputStream, ByteArrayOutputStream}
 
@@ -81,15 +81,16 @@ case class RVDTableReader(rvd: RVD, globals: IR, rt: RTable) extends TableReader
 
   override def isDistinctlyKeyed: Boolean = false
 
-  def rowRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+  override def rowRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
     VirtualTypeWithReq.subset(requestedType.rowType, rt.rowType)
 
-  def globalRequiredness(ctx: ExecuteContext, requestedType: TableType): VirtualTypeWithReq =
+  override def globalRequiredness(ctx: ExecuteContext, requestedType: TableType)
+    : VirtualTypeWithReq =
     VirtualTypeWithReq.subset(requestedType.globalType, rt.globalType)
 
   override def toJValue: JValue = JString("RVDTableReader")
 
-  def renderShort(): String = "RVDTableReader"
+  override def renderShort(): String = "RVDTableReader"
 
   override def defaultRender(): String = "RVDTableReader"
 
diff --git a/hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala b/hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala
index d6da5b5ba97..4f939f7683c 100644
--- a/hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala
+++ b/hail/hail/src/is/hail/expr/ir/lowering/TableStageDependency.scala
@@ -1,7 +1,7 @@
 package is.hail.expr.ir.lowering
 
+import is.hail.collection.FastSeq
 import is.hail.rvd.RVD
-import is.hail.utils.FastSeq
 
 trait DependencySource
 
diff --git a/hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala b/hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala
index 3d56a5a38e1..9fd78320394 100644
--- a/hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala
+++ b/hail/hail/src/is/hail/expr/ir/ndarrays/EmitNDArray.scala
@@ -2,6 +2,8 @@ package is.hail.expr.ir.ndarrays
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs.{
   NDArrayAgg, NDArrayConcat, NDArrayFilter, NDArrayMap, NDArrayMap2, NDArrayReindex, NDArrayReshape,
@@ -11,8 +13,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual._
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 abstract class NDArrayProducer {
   outer =>
diff --git a/hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala
index 6436b8f67d7..c4220eeb0ec 100644
--- a/hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala
+++ b/hail/hail/src/is/hail/expr/ir/orderings/BinaryOrdering.scala
@@ -13,7 +13,7 @@ object BinaryOrdering {
       val type1: SBinary = t1
       val type2: SBinary = t2
 
-      def _compareNonnull(cb: EmitCodeBuilder, x: SValue, y: SValue): Value[Int] = {
+      override def _compareNonnull(cb: EmitCodeBuilder, x: SValue, y: SValue): Value[Int] = {
         val xv: SBinaryValue = x.asBinary
         val yv: SBinaryValue = y.asBinary
         val xlen = xv.loadLength(cb)
diff --git a/hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala b/hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala
index 25dba617b20..383f0f09336 100644
--- a/hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala
+++ b/hail/hail/src/is/hail/expr/ir/orderings/CodeOrdering.scala
@@ -1,12 +1,12 @@
 package is.hail.expr.ir.orderings
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCodeBuilder, EmitValue}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object CodeOrdering {
 
diff --git a/hail/hail/src/is/hail/expr/ir/package.scala b/hail/hail/src/is/hail/expr/ir/package.scala
index 53714ab1bfe..1753d89a17d 100644
--- a/hail/hail/src/is/hail/expr/ir/package.scala
+++ b/hail/hail/src/is/hail/expr/ir/package.scala
@@ -1,20 +1,26 @@
 package is.hail.expr
 
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.IRFunctionRegistry
 import is.hail.expr.ir.lowering.TableStageDependency
 import is.hail.rvd.RVDPartitioner
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.tcoerce
 import is.hail.types.virtual._
 import is.hail.types.virtual.TIterable.elementType
-import is.hail.utils._
+import is.hail.utils.fatal
 
 import scala.collection.BufferedIterator
 
 import java.util.UUID
 
+import org.apache.commons.lang3.StringUtils
+import org.apache.spark.TaskContext
+
 package object ir {
   type TokenIterator = BufferedIterator[Token]
   type IEmitCode = IEmitCodeGen[SValue]
@@ -31,8 +37,6 @@ package object ir {
 
   def uuid4(): String = UUID.randomUUID().toString
 
-  def genSym(base: String): Sym = Sym.gen(base)
-
   // Build consistent expression for a filter-condition with keep polarity,
   // using Let to manage missing-ness.
   def filterPredicateWithKeep(irPred: IR, keep: Boolean): IR =
@@ -41,7 +45,7 @@ package object ir {
     }
 
   def invoke(name: String, rt: Type, typeArgs: Seq[Type], errorID: Int, args: IR*): IR =
-    IRFunctionRegistry.lookupUnseeded(name, rt, typeArgs, args.map(_.typ)) match {
+    IRFunctionRegistry.lookup(name, rt, typeArgs, args.map(_.typ)) match {
       case Some(f) => f(args, errorID)
       case None => fatal(
           s"no conversion found for $name[${typeArgs.mkString(", ")}](${args.map(_.typ).mkString(", ")}) => $rt"
@@ -57,13 +61,6 @@ package object ir {
   def invoke(name: String, rt: Type, errorID: Int, args: IR*): IR =
     invoke(name, rt, Array.empty[Type], errorID, args: _*)
 
-  def invokeSeeded(name: String, staticUID: Long, rt: Type, rngState: IR, args: IR*): IR =
-    IRFunctionRegistry.lookupSeeded(name, staticUID, rt, args.map(_.typ)) match {
-      case Some(f) => f(args, rngState)
-      case None =>
-        fatal(s"no seeded function found for $name(${args.map(_.typ).mkString(", ")}) => $rt")
-    }
-
   implicit def irToPrimitiveIR(ir: IR): PrimitiveIR = new PrimitiveIR(ir)
 
   implicit def intToIR(i: Int): I32 = I32(i)
@@ -424,6 +421,15 @@ package object ir {
 
   def logIR(result: IR, messages: AnyRef*): IR = ConsoleLog(strConcat(messages: _*), result)
 
+  def partFile(numDigits: Int, i: Int): String = {
+    val is = i.toString
+    assert(is.length <= numDigits)
+    "part-" + StringUtils.leftPad(is, numDigits, "0")
+  }
+
+  def partFile(d: Int, i: Int, ctx: TaskContext): String =
+    s"${partFile(d, i)}-${ctx.partSuffix}"
+
   implicit def toRichIndexedSeqEmitSettable(s: IndexedSeq[EmitSettable])
     : RichIndexedSeqEmitSettable = new RichIndexedSeqEmitSettable(s)
 
diff --git a/hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala b/hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala
index a089441a318..e414cc2f56a 100644
--- a/hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala
+++ b/hail/hail/src/is/hail/expr/ir/streams/EmitStream.scala
@@ -3,6 +3,9 @@ package is.hail.expr.ir.streams
 import is.hail.annotations.{Region, RegionPool}
 import is.hail.annotations.Region.REGULAR
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichOption
 import is.hail.expr.ir._
 import is.hail.expr.ir.agg.{AggStateSig, DictState, PhysicalAggSig, StateTuple}
 import is.hail.expr.ir.defs._
@@ -24,6 +27,7 @@ import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.{SFloat64Value, SInt32Value}
 import is.hail.types.virtual._
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 import is.hail.variant.Locus
 
 import scala.annotation.nowarn
@@ -422,7 +426,7 @@ object EmitStream {
 
                 val element: EmitCode = EmitCode.fromI(mb)(cb => container.loadElement(cb, idx))
 
-                def close(cb: EmitCodeBuilder): Unit = {}
+                override def close(cb: EmitCodeBuilder): Unit = {}
               }
             )
 
@@ -669,7 +673,7 @@ object EmitStream {
 
                 val element: EmitCode = eltField.load
 
-                def close(cb: EmitCodeBuilder): Unit = {}
+                override def close(cb: EmitCodeBuilder): Unit = {}
               }
             ),
           )
@@ -793,7 +797,7 @@ object EmitStream {
 
                 val element: EmitCode = EmitCode.present(mb, new SInt32Value(curr))
 
-                def close(cb: EmitCodeBuilder): Unit = {}
+                override def close(cb: EmitCodeBuilder): Unit = {}
               }
               SStreamValue(producer)
 
@@ -864,7 +868,7 @@ object EmitStream {
 
                 val element: EmitCode = EmitCode.present(mb, new SInt32Value(curr))
 
-                def close(cb: EmitCodeBuilder): Unit = {}
+                override def close(cb: EmitCodeBuilder): Unit = {}
               }
 
               SStreamValue(producer)
@@ -940,7 +944,7 @@ object EmitStream {
 
                   val element: EmitCode = EmitCode.present(mb, new SInt32Value(curr))
 
-                  def close(cb: EmitCodeBuilder): Unit = {}
+                  override def close(cb: EmitCodeBuilder): Unit = {}
                 }
 
                 SStreamValue(producer)
@@ -1074,7 +1078,7 @@ object EmitStream {
 
                 val element: EmitCode = elementField
 
-                def close(cb: EmitCodeBuilder): Unit = {
+                override def close(cb: EmitCodeBuilder): Unit = {
                   childProducer.close(cb)
                   if (requiresMemoryManagementPerElement)
                     cb += childProducer.elementRegion.invalidate()
@@ -1339,7 +1343,7 @@ object EmitStream {
 
                 val element: EmitCode = bodyResult
 
-                def close(cb: EmitCodeBuilder): Unit = childProducer.close(cb)
+                override def close(cb: EmitCodeBuilder): Unit = childProducer.close(cb)
               }
 
               mb.implementLabel(childProducer.LendOfStream)(cb => cb.goto(producer.LendOfStream))
@@ -1725,7 +1729,7 @@ object EmitStream {
               }
               val element: EmitCode = innerProducer.element
 
-              def close(cb: EmitCodeBuilder): Unit = {
+              override def close(cb: EmitCodeBuilder): Unit = {
                 cb.if_(
                   innerUnclosed, {
                     cb.assign(innerUnclosed, false)
@@ -2935,7 +2939,7 @@ object EmitStream {
 
                     val element: EmitCode = bodyCode
 
-                    def close(cb: EmitCodeBuilder): Unit =
+                    override def close(cb: EmitCodeBuilder): Unit =
                       producers.foreach(_.close(cb))
                   }
 
@@ -3028,7 +3032,7 @@ object EmitStream {
 
                     val element: EmitCode = bodyCode
 
-                    def close(cb: EmitCodeBuilder): Unit =
+                    override def close(cb: EmitCodeBuilder): Unit =
                       producers.foreach(_.close(cb))
                   }
 
@@ -3107,7 +3111,7 @@ object EmitStream {
 
                     val element: EmitCode = bodyCode
 
-                    def close(cb: EmitCodeBuilder): Unit =
+                    override def close(cb: EmitCodeBuilder): Unit =
                       producers.foreach(_.close(cb))
                   }
 
@@ -3854,7 +3858,7 @@ object EmitStream {
               val elementField = mb.newEmitField(elementType)
 
               val producer = new StreamProducer {
-                def method: EmitMethodBuilder[_] = mb
+                override def method: EmitMethodBuilder[_] = mb
 
                 val length: Option[EmitCodeBuilder => Code[Int]] = None
 
@@ -3865,7 +3869,7 @@ object EmitStream {
                 val requiresMemoryManagementPerElement: Boolean =
                   childProducer.requiresMemoryManagementPerElement
 
-                def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
+                override def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
                   cb.assign(queueSize, emit(maxQueueSize, cb).getOrAssert(cb).asInt32.value)
                   cb.assign(
                     queue,
@@ -3955,7 +3959,7 @@ object EmitStream {
                   cb.goto(childProducer.LproduceElement)
                 }
 
-                def close(cb: EmitCodeBuilder): Unit = childProducer.close(cb)
+                override def close(cb: EmitCodeBuilder): Unit = childProducer.close(cb)
               }
 
               mb.implementLabel(childProducer.LendOfStream)(cb => cb.goto(producer.LendOfStream))
diff --git a/hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala b/hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala
index 9f811bf717e..24e9acc48d7 100644
--- a/hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala
+++ b/hail/hail/src/is/hail/expr/ir/streams/StagedMinHeap.scala
@@ -2,12 +2,12 @@ package is.hail.expr.ir.streams
 
 import is.hail.annotations.{Region, RegionPool}
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitClassBuilder, EmitCodeBuilder, EmitMethodBuilder, EmitModuleBuilder}
 import is.hail.expr.ir.agg.StagedArrayBuilder
 import is.hail.types.physical.PCanonicalArray
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
-import is.hail.utils.FastSeq
 
 sealed trait StagedMinHeap {
   def arraySType: SType
diff --git a/hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala b/hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala
index 80bf7dd0774..0402ec52003 100644
--- a/hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala
+++ b/hail/hail/src/is/hail/expr/ir/streams/StreamUtils.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.streams
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{codeToRichCodeRegion, valueToRichCodeRegion}
 import is.hail.expr.ir.{
   EmitCode, EmitCodeBuilder, EmitMethodBuilder, IEmitCode, IR, Name, StagedArrayBuilder,
 }
@@ -254,7 +255,7 @@ object StreamUtils {
 
     def implInit(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit
 
-    final def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
+    final override def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
       implInit(cb, outerRegion)
       cb.assign(bracket, Code.newArray[Int](k))
       cb.assign(heads, Code.newArray[Long](k))
@@ -265,7 +266,7 @@ object StreamUtils {
 
     def implClose(cb: EmitCodeBuilder): Unit
 
-    final def close(cb: EmitCodeBuilder): Unit = {
+    final override def close(cb: EmitCodeBuilder): Unit = {
       implClose(cb)
       cb.assign(bracket, Code._null)
       cb.assign(heads, Code._null)
diff --git a/hail/hail/src/is/hail/io/ArrayImpex.scala b/hail/hail/src/is/hail/io/ArrayImpex.scala
new file mode 100644
index 00000000000..cfee794c3b4
--- /dev/null
+++ b/hail/hail/src/is/hail/io/ArrayImpex.scala
@@ -0,0 +1,23 @@
+package is.hail.io
+
+import is.hail.io.fs.FS
+import is.hail.utils.using
+
+object ArrayImpex {
+  val DefaultBuffSize: Int = 4096 << 3
+
+  def importFromDoubles(fs: FS, path: String, n: Int): Array[Double] = {
+    val a = new Array[Double](n)
+    importFromDoubles(fs, path, a, DefaultBuffSize)
+    a
+  }
+
+  def importFromDoubles(fs: FS, path: String, a: Array[Double], bufSize: Int): Unit =
+    using(new DoubleInputBuffer(fs.open(path), bufSize))(_.readDoubles(a))
+
+  def exportToDoubles(fs: FS, path: String, a: Array[Double]): Unit =
+    exportToDoubles(fs, path, a, DefaultBuffSize)
+
+  def exportToDoubles(fs: FS, path: String, a: Array[Double], bufSize: Int): Unit =
+    using(new DoubleOutputBuffer(fs.create(path), bufSize))(_.writeDoubles(a))
+}
diff --git a/hail/hail/src/is/hail/io/BufferSpecs.scala b/hail/hail/src/is/hail/io/BufferSpecs.scala
index 76561cfcafb..7930caf17b8 100644
--- a/hail/hail/src/is/hail/io/BufferSpecs.scala
+++ b/hail/hail/src/is/hail/io/BufferSpecs.scala
@@ -89,35 +89,35 @@ trait BufferSpec extends Spec {
 }
 
 final case class LEB128BufferSpec(child: BufferSpec) extends BufferSpec {
-  def buildInputBuffer(in: InputStream): InputBuffer =
+  override def buildInputBuffer(in: InputStream): InputBuffer =
     new LEB128InputBuffer(child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBuffer =
     new LEB128OutputBuffer(child.buildOutputBuffer(out))
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
     Code.newInstance[LEB128InputBuffer, InputBuffer](child.buildCodeInputBuffer(in))
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
     Code.newInstance[LEB128OutputBuffer, OutputBuffer](child.buildCodeOutputBuffer(out))
 }
 
 final case class BlockingBufferSpec(blockSize: Int, child: BlockBufferSpec) extends BufferSpec {
   require(blockSize <= (1 << 16))
 
-  def buildInputBuffer(in: InputStream): InputBuffer =
+  override def buildInputBuffer(in: InputStream): InputBuffer =
     new BlockingInputBuffer(blockSize, child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBuffer =
     new BlockingOutputBuffer(blockSize, child.buildOutputBuffer(out))
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
     Code.newInstance[BlockingInputBuffer, Int, InputBlockBuffer](
       blockSize,
       child.buildCodeInputBuffer(in),
     )
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
     Code.newInstance[BlockingOutputBuffer, Int, OutputBlockBuffer](
       blockSize,
       child.buildCodeOutputBuffer(out),
@@ -147,20 +147,20 @@ abstract class LZ4BlockBufferSpecCommon extends BlockBufferSpec {
 
   def child: BlockBufferSpec
 
-  def buildInputBuffer(in: InputStream): InputBlockBuffer =
+  override def buildInputBuffer(in: InputStream): InputBlockBuffer =
     new LZ4InputBlockBuffer(lz4, blockSize, child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
     new LZ4OutputBlockBuffer(lz4, blockSize, child.buildOutputBuffer(out))
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
     Code.newInstance[LZ4InputBlockBuffer, LZ4, Int, InputBlockBuffer](
       stagedlz4,
       blockSize,
       child.buildCodeInputBuffer(in),
     )
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
     Code.newInstance[LZ4OutputBlockBuffer, LZ4, Int, OutputBlockBuffer](
       stagedlz4,
       blockSize,
@@ -170,16 +170,16 @@ abstract class LZ4BlockBufferSpecCommon extends BlockBufferSpec {
 
 final case class LZ4HCBlockBufferSpec(blockSize: Int, child: BlockBufferSpec)
     extends LZ4BlockBufferSpecCommon {
-  def lz4 = LZ4.hc
-  def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "hc")
-  def typeName = "LZ4HCBlockBufferSpec"
+  override def lz4 = LZ4.hc
+  override def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "hc")
+  override def typeName = "LZ4HCBlockBufferSpec"
 }
 
 final case class LZ4FastBlockBufferSpec(blockSize: Int, child: BlockBufferSpec)
     extends LZ4BlockBufferSpecCommon {
-  def lz4 = LZ4.fast
-  def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "fast")
-  def typeName = "LZ4FastBlockBufferSpec"
+  override def lz4 = LZ4.fast
+  override def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "fast")
+  override def typeName = "LZ4FastBlockBufferSpec"
 }
 
 final case class LZ4SizeBasedBlockBufferSpec(
@@ -196,10 +196,10 @@ final case class LZ4SizeBasedBlockBufferSpec(
   def stagedlz4: Code[LZ4] = Code.invokeScalaObject0[LZ4](LZ4.getClass, "fast")
   def typeName = "LZ4SizeBasedBlockBufferSpec"
 
-  def buildInputBuffer(in: InputStream): InputBlockBuffer =
+  override def buildInputBuffer(in: InputStream): InputBlockBuffer =
     new LZ4SizeBasedCompressingInputBlockBuffer(lz4, blockSize, child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
     new LZ4SizeBasedCompressingOutputBlockBuffer(
       lz4,
       blockSize,
@@ -207,14 +207,14 @@ final case class LZ4SizeBasedBlockBufferSpec(
       child.buildOutputBuffer(out),
     )
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
     Code.newInstance[LZ4SizeBasedCompressingInputBlockBuffer, LZ4, Int, InputBlockBuffer](
       stagedlz4,
       blockSize,
       child.buildCodeInputBuffer(in),
     )
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
     Code.newInstance[LZ4SizeBasedCompressingOutputBlockBuffer, LZ4, Int, Int, OutputBlockBuffer](
       stagedlz4,
       blockSize,
@@ -227,19 +227,19 @@ final case class ZstdBlockBufferSpec(blockSize: Int, child: BlockBufferSpec)
     extends BlockBufferSpec {
   require(blockSize <= (1 << 16))
 
-  def buildInputBuffer(in: InputStream): InputBlockBuffer =
+  override def buildInputBuffer(in: InputStream): InputBlockBuffer =
     new ZstdInputBlockBuffer(blockSize, child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
     new ZstdOutputBlockBuffer(blockSize, child.buildOutputBuffer(out))
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
     Code.newInstance[ZstdInputBlockBuffer, Int, InputBlockBuffer](
       blockSize,
       child.buildCodeInputBuffer(in),
     )
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
     Code.newInstance[ZstdOutputBlockBuffer, Int, OutputBlockBuffer](
       blockSize,
       child.buildCodeOutputBuffer(out),
@@ -253,19 +253,19 @@ final case class ZstdSizedBasedBlockBufferSpec(
 ) extends BlockBufferSpec {
   require(blockSize <= (1 << 16))
 
-  def buildInputBuffer(in: InputStream): InputBlockBuffer =
+  override def buildInputBuffer(in: InputStream): InputBlockBuffer =
     new ZstdSizedBasedInputBlockBuffer(blockSize, child.buildInputBuffer(in))
 
-  def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
+  override def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
     new ZstdSizedBasedOutputBlockBuffer(blockSize, minCompressionSize, child.buildOutputBuffer(out))
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
     Code.newInstance[ZstdSizedBasedInputBlockBuffer, Int, InputBlockBuffer](
       blockSize,
       child.buildCodeInputBuffer(in),
     )
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
     Code.newInstance[ZstdSizedBasedOutputBlockBuffer, Int, Int, OutputBlockBuffer](
       blockSize,
       minCompressionSize,
@@ -278,14 +278,15 @@ object StreamBlockBufferSpec {
 }
 
 final class StreamBlockBufferSpec extends BlockBufferSpec {
-  def buildInputBuffer(in: InputStream): InputBlockBuffer = new StreamBlockInputBuffer(in)
+  override def buildInputBuffer(in: InputStream): InputBlockBuffer = new StreamBlockInputBuffer(in)
 
-  def buildOutputBuffer(out: OutputStream): OutputBlockBuffer = new StreamBlockOutputBuffer(out)
+  override def buildOutputBuffer(out: OutputStream): OutputBlockBuffer =
+    new StreamBlockOutputBuffer(out)
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBlockBuffer] =
     Code.newInstance[StreamBlockInputBuffer, InputStream](in)
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBlockBuffer] =
     Code.newInstance[StreamBlockOutputBuffer, OutputStream](out)
 
   override def equals(other: Any): Boolean = other.isInstanceOf[StreamBlockBufferSpec]
@@ -296,10 +297,10 @@ final class StreamBufferSpec extends BufferSpec {
 
   override def buildOutputBuffer(out: OutputStream): OutputBuffer = new StreamOutputBuffer(out)
 
-  def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
+  override def buildCodeInputBuffer(in: Code[InputStream]): Code[InputBuffer] =
     Code.newInstance[StreamInputBuffer, InputStream](in)
 
-  def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
+  override def buildCodeOutputBuffer(out: Code[OutputStream]): Code[OutputBuffer] =
     Code.newInstance[StreamOutputBuffer, OutputStream](out)
 
   override def equals(other: Any): Boolean = other.isInstanceOf[StreamBufferSpec]
diff --git a/hail/hail/src/is/hail/io/ByteArrayReader.scala b/hail/hail/src/is/hail/io/ByteArrayReader.scala
index a48a2189035..d5eece2237f 100644
--- a/hail/hail/src/is/hail/io/ByteArrayReader.scala
+++ b/hail/hail/src/is/hail/io/ByteArrayReader.scala
@@ -27,7 +27,7 @@ class ByteArrayReader(val arr: Array[Byte]) extends AbstractBinaryReader {
   def seek(pos: Int): Unit =
     position = pos
 
-  def skipBytes(bytes: Long): Long = {
+  override def skipBytes(bytes: Long): Long = {
     require(bytes < Integer.MAX_VALUE)
     position += bytes.toInt
     if (position < length)
diff --git a/hail/hail/src/is/hail/io/CodecSpec.scala b/hail/hail/src/is/hail/io/CodecSpec.scala
index 328234c837f..3a017448f03 100644
--- a/hail/hail/src/is/hail/io/CodecSpec.scala
+++ b/hail/hail/src/is/hail/io/CodecSpec.scala
@@ -7,8 +7,7 @@ import is.hail.sparkextras.ContextRDD
 import is.hail.types.encoded.EType
 import is.hail.types.physical.PType
 import is.hail.types.virtual.Type
-import is.hail.utils.{using, ArrayOfByteArrayOutputStream}
-import is.hail.utils.prettyPrint.ArrayOfByteArrayInputStream
+import is.hail.utils.{using, ArrayOfByteArrayInputStream, ArrayOfByteArrayOutputStream}
 
 import java.io.{ByteArrayInputStream, ByteArrayOutputStream, InputStream, OutputStream}
 
diff --git a/hail/hail/src/is/hail/io/Decoder.scala b/hail/hail/src/is/hail/io/Decoder.scala
index 25a5d9452fa..0ad0d158b7e 100644
--- a/hail/hail/src/is/hail/io/Decoder.scala
+++ b/hail/hail/src/is/hail/io/Decoder.scala
@@ -9,8 +9,6 @@ import is.hail.utils.RestartableByteArrayInputStream
 import java.io._
 
 trait Decoder extends Closeable {
-  def close(): Unit
-
   def ptype: PType
 
   def readRegionValue(region: Region): Long
@@ -26,17 +24,17 @@ final class CompiledDecoder(
   theHailClassLoader: HailClassLoader,
   f: (HailClassLoader) => DecoderAsmFunction,
 ) extends Decoder {
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def readByte(): Byte = in.readByte()
+  override def readByte(): Byte = in.readByte()
 
   private[this] val compiled = f(theHailClassLoader)
 
-  def readRegionValue(r: Region): Long =
+  override def readRegionValue(r: Region): Long =
     compiled(r, in)
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 }
 
 final class ByteArrayDecoder(
diff --git a/hail/hail/src/is/hail/io/DoubleInputBuffer.scala b/hail/hail/src/is/hail/io/DoubleInputBuffer.scala
index 2770606d7d5..93cfacf7d26 100644
--- a/hail/hail/src/is/hail/io/DoubleInputBuffer.scala
+++ b/hail/hail/src/is/hail/io/DoubleInputBuffer.scala
@@ -1,7 +1,7 @@
 package is.hail.io
 
 import is.hail.annotations.Memory
-import is.hail.utils._
+import is.hail.utils.implicits.toRichInputStream
 
 import java.io.{Closeable, InputStream, OutputStream}
 
@@ -10,7 +10,7 @@ final class DoubleInputBuffer(in: InputStream, bufSize: Int) extends Closeable {
   private var end: Int = 0
   private var off: Int = 0
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
   def readDoubles(to: Array[Double]): Unit = readDoubles(to, 0, to.length)
@@ -45,7 +45,7 @@ final class DoubleOutputBuffer(out: OutputStream, bufSize: Int) extends Closeabl
   private val buf: Array[Byte] = new Array[Byte](bufSize)
   private var off: Int = 0
 
-  def close(): Unit = {
+  override def close(): Unit = {
     flush()
     out.close()
   }
diff --git a/hail/hail/src/is/hail/io/Encoder.scala b/hail/hail/src/is/hail/io/Encoder.scala
index 6e0a43dd0a4..6d63b27c4a5 100644
--- a/hail/hail/src/is/hail/io/Encoder.scala
+++ b/hail/hail/src/is/hail/io/Encoder.scala
@@ -10,7 +10,7 @@ import java.io._
 trait Encoder extends Closeable {
   def flush(): Unit
 
-  def close(): Unit
+  override def close(): Unit
 
   def writeRegionValue(region: Region, offset: Long): Unit
 
@@ -28,10 +28,10 @@ final class CompiledEncoder(
   private[this] var partitionRegion: Region = _
   private[this] val compiled = f(theHailClassLoader)
 
-  def flush(): Unit =
+  override def flush(): Unit =
     out.flush()
 
-  def close(): Unit = {
+  override def close(): Unit = {
     compiled.asInstanceOf[FunctionWithPartitionRegion].setPool(null)
     compiled.asInstanceOf[FunctionWithPartitionRegion].addPartitionRegion(null)
     if (partitionRegion != null) partitionRegion.close()
@@ -45,7 +45,7 @@ final class CompiledEncoder(
     poolSet = true
   }
 
-  def writeRegionValue(r: Region, offset: Long): Unit = {
+  override def writeRegionValue(r: Region, offset: Long): Unit = {
     setScratchPool(r.pool)
     writeRegionValue(offset)
   }
@@ -55,10 +55,10 @@ final class CompiledEncoder(
     compiled(offset, out)
   }
 
-  def writeByte(b: Byte): Unit =
+  override def writeByte(b: Byte): Unit =
     out.writeByte(b)
 
-  def indexOffset(): Long = out.indexOffset()
+  override def indexOffset(): Long = out.indexOffset()
 }
 
 final class ByteArrayEncoder(
@@ -68,7 +68,7 @@ final class ByteArrayEncoder(
   private[this] val baos = new ByteArrayOutputStream()
   private[this] val enc = makeEnc(baos, theHailClassLoader)
 
-  def close(): Unit = {
+  override def close(): Unit = {
     enc.close()
     baos.close()
   }
diff --git a/hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala b/hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala
index 0a556280f1f..1fdfcc0c972 100644
--- a/hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala
+++ b/hail/hail/src/is/hail/io/HadoopFSDataBinaryReader.scala
@@ -10,11 +10,11 @@ class HadoopFSDataBinaryReader(fis: SeekableDataInputStream)
   override def read(byteArray: Array[Byte], hasRead: Int, toRead: Int): Int =
     fis.read(byteArray, hasRead, toRead)
 
-  def close(): Unit = fis.close()
+  override def close(): Unit = fis.close()
 
   def seek(pos: Long): Unit = fis.seek(pos)
 
-  def skipBytes(bytes: Long): Long = fis.skip(bytes)
+  override def skipBytes(bytes: Long): Long = fis.skip(bytes)
 
   def getPosition: Long = fis.getPosition
 }
diff --git a/hail/hail/src/is/hail/io/IndexBTree.scala b/hail/hail/src/is/hail/io/IndexBTree.scala
index b45babfc995..92dfc50dc4e 100644
--- a/hail/hail/src/is/hail/io/IndexBTree.scala
+++ b/hail/hail/src/is/hail/io/IndexBTree.scala
@@ -108,7 +108,7 @@ class IndexBTree(indexFileName: String, fs: FS, branchingFactor: Int = 1024) ext
         )
     }
 
-  def close(): Unit = is.close()
+  override def close(): Unit = is.close()
 
   def calcDepth(): Int =
     IndexBTree.calcDepth(fs.getFileSize(indexFileName) / 8, branchingFactor)
diff --git a/hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala b/hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala
index beef7d2c48d..bbff8bcb57f 100644
--- a/hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala
+++ b/hail/hail/src/is/hail/io/IndexedBinaryBlockReader.scala
@@ -44,18 +44,18 @@ abstract class IndexedBinaryBlockReader[T](job: Configuration, split: FileSplit)
     )
   }
 
-  def createKey(): LongWritable = new LongWritable()
+  override def createKey(): LongWritable = new LongWritable()
 
-  def createValue(): T
+  override def createValue(): T
 
-  def getPos: Long = pos
+  override def getPos: Long = pos
 
-  def getProgress: Float =
+  override def getProgress: Float =
     if (partitionStart == end)
       0.0f
     else
       Math.min(1.0f, (pos - partitionStart) / (end - partitionStart).toFloat)
 
-  def close() = bfis.close()
+  override def close() = bfis.close()
 
 }
diff --git a/hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala b/hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala
index c07d6608111..b5da9a743c1 100644
--- a/hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala
+++ b/hail/hail/src/is/hail/io/IndexedBinaryInputFormat.scala
@@ -5,6 +5,6 @@ import org.apache.hadoop.mapred._
 
 abstract class IndexedBinaryInputFormat[T] extends FileInputFormat[LongWritable, T] {
 
-  def getRecordReader(split: InputSplit, job: JobConf, reporter: Reporter)
+  override def getRecordReader(split: InputSplit, job: JobConf, reporter: Reporter)
     : RecordReader[LongWritable, T]
 }
diff --git a/hail/hail/src/is/hail/io/InputBuffers.scala b/hail/hail/src/is/hail/io/InputBuffers.scala
index e6d6c62af8b..d8519c8c137 100644
--- a/hail/hail/src/is/hail/io/InputBuffers.scala
+++ b/hail/hail/src/is/hail/io/InputBuffers.scala
@@ -3,6 +3,7 @@ package is.hail.io
 import is.hail.annotations.{Memory, Region}
 import is.hail.io.compress.LZ4
 import is.hail.utils._
+import is.hail.utils.implicits.toRichInputStream
 
 import java.io._
 import java.util.UUID
@@ -11,7 +12,7 @@ import java.util.function.Supplier
 import com.github.luben.zstd.{Zstd, ZstdDecompressCtx}
 
 trait InputBuffer extends Closeable {
-  def close(): Unit
+  override def close(): Unit
 
   def seek(offset: Long): Unit
 
@@ -59,7 +60,7 @@ trait InputBuffer extends Closeable {
 }
 
 trait InputBlockBuffer extends Spec with Closeable {
-  def close(): Unit
+  override def close(): Unit
 
   def seek(offset: Long): Unit
 
@@ -84,11 +85,11 @@ trait InputBlockBuffer extends Spec with Closeable {
 final class StreamInputBuffer(in: InputStream) extends InputBuffer {
   private[this] val buff = new Array[Byte](8)
 
-  def close(): Unit = in.close()
+  override def close(): Unit = in.close()
 
-  def seek(offset: Long) = in.asInstanceOf[ByteTrackingInputStream].seek(offset)
+  override def seek(offset: Long) = in.asInstanceOf[ByteTrackingInputStream].seek(offset)
 
-  def readByte(): Byte = {
+  override def readByte(): Byte = {
     in.readFully(buff, 0, 1)
     Memory.loadByte(buff, 0)
   }
@@ -96,63 +97,63 @@ final class StreamInputBuffer(in: InputStream) extends InputBuffer {
   override def read(buf: Array[Byte], toOff: Int, n: Int): Unit =
     in.readFully(buf, toOff, n)
 
-  def readInt(): Int = {
+  override def readInt(): Int = {
     in.readFully(buff, 0, 4)
     Memory.loadInt(buff, 0)
   }
 
-  def readLong(): Long = {
+  override def readLong(): Long = {
     in.readFully(buff)
     Memory.loadLong(buff, 0)
   }
 
-  def readFloat(): Float = {
+  override def readFloat(): Float = {
     in.readFully(buff, 0, 4)
     Memory.loadFloat(buff, 0)
   }
 
-  def readDouble(): Double = {
+  override def readDouble(): Double = {
     in.readFully(buff)
     Memory.loadDouble(buff, 0)
   }
 
-  def readBytes(toRegion: Region, toOff: Long, n: Int): Unit =
+  override def readBytes(toRegion: Region, toOff: Long, n: Int): Unit =
     Region.storeBytes(toOff, readBytesArray(n))
 
-  def readBytesArray(n: Int): Array[Byte] =
+  override def readBytesArray(n: Int): Array[Byte] =
     Array.tabulate(n)(_ => readByte())
 
-  def skipByte(): Unit = {
+  override def skipByte(): Unit = {
     val bytesRead = in.skip(1)
     assert(bytesRead == 1L)
   }
 
-  def skipInt(): Unit = {
+  override def skipInt(): Unit = {
     val bytesRead = in.skip(4)
     assert(bytesRead == 4L)
   }
 
-  def skipLong(): Unit = {
+  override def skipLong(): Unit = {
     val bytesRead = in.skip(8)
     assert(bytesRead == 8L)
   }
 
-  def skipFloat(): Unit = {
+  override def skipFloat(): Unit = {
     val bytesRead = in.skip(4)
     assert(bytesRead == 4L)
   }
 
-  def skipDouble(): Unit = {
+  override def skipDouble(): Unit = {
     val bytesRead = in.skip(8)
     assert(bytesRead == 8L)
   }
 
-  def skipBytes(n: Int): Unit = {
+  override def skipBytes(n: Int): Unit = {
     val bytesRead = in.skip(n.toLong)
     assert(bytesRead == n)
   }
 
-  def readDoubles(to: Array[Double], off: Int, n: Int): Unit = {
+  override def readDoubles(to: Array[Double], off: Int, n: Int): Unit = {
     var i = 0
     while (i < n) {
       to(off + i) = readDouble()
@@ -162,55 +163,55 @@ final class StreamInputBuffer(in: InputStream) extends InputBuffer {
 }
 
 final class MemoryInputBuffer(mb: MemoryBuffer) extends InputBuffer {
-  def close(): Unit = {}
+  override def close(): Unit = {}
 
-  def seek(offset: Long) = ???
+  override def seek(offset: Long) = ???
 
-  def readByte(): Byte = mb.readByte()
+  override def readByte(): Byte = mb.readByte()
 
-  def readInt(): Int = mb.readInt()
+  override def readInt(): Int = mb.readInt()
 
-  def readLong(): Long = mb.readLong()
+  override def readLong(): Long = mb.readLong()
 
-  def readFloat(): Float = mb.readFloat()
+  override def readFloat(): Float = mb.readFloat()
 
-  def readDouble(): Double = mb.readDouble()
+  override def readDouble(): Double = mb.readDouble()
 
-  def readBytes(toRegion: Region, toOff: Long, n: Int): Unit = mb.readBytes(toOff, n)
+  override def readBytes(toRegion: Region, toOff: Long, n: Int): Unit = mb.readBytes(toOff, n)
 
-  def readBytesArray(n: Int): Array[Byte] = {
+  override def readBytesArray(n: Int): Array[Byte] = {
     val arr = new Array[Byte](n)
     mb.readBytesArray(arr, n)
     arr
   }
 
-  def skipByte(): Unit = mb.skipByte()
+  override def skipByte(): Unit = mb.skipByte()
 
-  def skipInt(): Unit = mb.skipInt()
+  override def skipInt(): Unit = mb.skipInt()
 
-  def skipLong(): Unit = mb.skipLong()
+  override def skipLong(): Unit = mb.skipLong()
 
-  def skipFloat(): Unit = mb.skipFloat()
+  override def skipFloat(): Unit = mb.skipFloat()
 
-  def skipDouble(): Unit = mb.skipDouble()
+  override def skipDouble(): Unit = mb.skipDouble()
 
-  def skipBytes(n: Int): Unit = mb.skipBytes(n)
+  override def skipBytes(n: Int): Unit = mb.skipBytes(n)
 
-  def readDoubles(to: Array[Double], off: Int, n: Int): Unit = ???
+  override def readDoubles(to: Array[Double], off: Int, n: Int): Unit = ???
 }
 
 final class LEB128InputBuffer(in: InputBuffer) extends InputBuffer {
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 
-  def readByte(): Byte =
+  override def readByte(): Byte =
     in.readByte()
 
   override def read(buf: Array[Byte], toOff: Int, n: Int) = in.read(buf, toOff, n)
 
-  def readInt(): Int = {
+  override def readInt(): Int = {
     var b: Byte = readByte()
     var x: Int = b & 0x7f
     var shift: Int = 7
@@ -222,7 +223,7 @@ final class LEB128InputBuffer(in: InputBuffer) extends InputBuffer {
     x
   }
 
-  def readLong(): Long = {
+  override def readLong(): Long = {
     var b: Byte = readByte()
     var x: Long = b & 0x7fL
     var shift: Int = 7
@@ -234,35 +235,37 @@ final class LEB128InputBuffer(in: InputBuffer) extends InputBuffer {
     x
   }
 
-  def readFloat(): Float = in.readFloat()
+  override def readFloat(): Float = in.readFloat()
 
-  def readDouble(): Double = in.readDouble()
+  override def readDouble(): Double = in.readDouble()
 
-  def readBytes(toRegion: Region, toOff: Long, n: Int): Unit = in.readBytes(toRegion, toOff, n)
+  override def readBytes(toRegion: Region, toOff: Long, n: Int): Unit =
+    in.readBytes(toRegion, toOff, n)
 
-  def readBytesArray(n: Int): Array[Byte] = in.readBytesArray(n)
+  override def readBytesArray(n: Int): Array[Byte] = in.readBytesArray(n)
 
-  def skipByte(): Unit = in.skipByte()
+  override def skipByte(): Unit = in.skipByte()
 
-  def skipInt(): Unit = {
+  override def skipInt(): Unit = {
     var b: Byte = readByte()
     while ((b & 0x80) != 0)
       b = readByte()
   }
 
-  def skipLong(): Unit = {
+  override def skipLong(): Unit = {
     var b: Byte = readByte()
     while ((b & 0x80) != 0)
       b = readByte()
   }
 
-  def skipFloat(): Unit = in.skipFloat()
+  override def skipFloat(): Unit = in.skipFloat()
 
-  def skipDouble(): Unit = in.skipDouble()
+  override def skipDouble(): Unit = in.skipDouble()
 
-  def skipBytes(n: Int): Unit = in.skipBytes(n)
+  override def skipBytes(n: Int): Unit = in.skipBytes(n)
 
-  def readDoubles(to: Array[Double], toOff: Int, n: Int): Unit = in.readDoubles(to, toOff, n)
+  override def readDoubles(to: Array[Double], toOff: Int, n: Int): Unit =
+    in.readDoubles(to, toOff, n)
 }
 
 final class TracingInputBuffer(
@@ -272,11 +275,11 @@ final class TracingInputBuffer(
   private[this] val logfile = new FileOutputStream(filename, true)
   logger.info(s"tracing to $filename")
 
-  def close(): Unit = in.close()
+  override def close(): Unit = in.close()
 
-  def seek(offset: Long): Unit = ???
+  override def seek(offset: Long): Unit = ???
 
-  def readByte(): Byte = {
+  override def readByte(): Byte = {
     val x = in.readByte()
     logfile.write(x.toInt)
     x
@@ -290,53 +293,53 @@ final class TracingInputBuffer(
     }
   }
 
-  def readInt(): Int = {
+  override def readInt(): Int = {
     val bytes = readBytesArray(4)
     Memory.loadInt(bytes, 0)
   }
 
-  def readLong(): Long = {
+  override def readLong(): Long = {
     val bytes = readBytesArray(8)
     Memory.loadLong(bytes, 0)
   }
 
-  def readFloat(): Float = {
+  override def readFloat(): Float = {
     val bytes = readBytesArray(4)
     Memory.loadFloat(bytes, 0)
   }
 
-  def readDouble(): Double = {
+  override def readDouble(): Double = {
     val bytes = readBytesArray(8)
     Memory.loadDouble(bytes, 0)
   }
 
-  def readBytes(toRegion: Region, toOff: Long, n: Int): Unit =
+  override def readBytes(toRegion: Region, toOff: Long, n: Int): Unit =
     Region.storeBytes(toOff, readBytesArray(n))
 
-  def readBytesArray(n: Int): Array[Byte] =
+  override def readBytesArray(n: Int): Array[Byte] =
     Array.tabulate(n)(_ => readByte())
 
   override def skipBoolean(): Unit = skipByte()
 
-  def skipByte(): Unit =
+  override def skipByte(): Unit =
     skipBytes(1)
 
-  def skipInt(): Unit =
+  override def skipInt(): Unit =
     skipBytes(4)
 
-  def skipLong(): Unit =
+  override def skipLong(): Unit =
     skipBytes(8)
 
-  def skipFloat(): Unit =
+  override def skipFloat(): Unit =
     skipBytes(4)
 
-  def skipDouble(): Unit =
+  override def skipDouble(): Unit =
     skipBytes(8)
 
-  @inline def skipBytes(n: Int): Unit =
+  @inline override def skipBytes(n: Int): Unit =
     for (_ <- 0 until n) readByte()
 
-  def readDoubles(to: Array[Double], off: Int, n: Int): Unit = {
+  override def readDoubles(to: Array[Double], off: Int, n: Int): Unit = {
     var i = 0
     while (i < n) {
       to(off + i) = readDouble()
@@ -363,52 +366,52 @@ final class BlockingInputBuffer(blockSize: Int, in: InputBlockBuffer) extends In
     assert(off + n <= end)
   }
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = {
+  override def seek(offset: Long): Unit = {
     in.seek(offset)
     end = in.readBlock(buf)
     off = (offset & 0xffff).asInstanceOf[Int]
     assert(off <= end)
   }
 
-  def readByte(): Byte = {
+  override def readByte(): Byte = {
     ensure(1)
     val b = Memory.loadByte(buf, off.toLong)
     off += 1
     b
   }
 
-  def readInt(): Int = {
+  override def readInt(): Int = {
     ensure(4)
     val i = Memory.loadInt(buf, off.toLong)
     off += 4
     i
   }
 
-  def readLong(): Long = {
+  override def readLong(): Long = {
     ensure(8)
     val l = Memory.loadLong(buf, off.toLong)
     off += 8
     l
   }
 
-  def readFloat(): Float = {
+  override def readFloat(): Float = {
     ensure(4)
     val f = Memory.loadFloat(buf, off.toLong)
     off += 4
     f
   }
 
-  def readDouble(): Double = {
+  override def readDouble(): Double = {
     ensure(8)
     val d = Memory.loadDouble(buf, off.toLong)
     off += 8
     d
   }
 
-  def readBytes(toRegion: Region, toOff0: Long, n0: Int): Unit = {
+  override def readBytes(toRegion: Region, toOff0: Long, n0: Int): Unit = {
     assert(n0 >= 0)
     var toOff = toOff0
     var n = n0
@@ -445,38 +448,38 @@ final class BlockingInputBuffer(blockSize: Int, in: InputBlockBuffer) extends In
     }
   }
 
-  def readBytesArray(n: Int): Array[Byte] = {
+  override def readBytesArray(n: Int): Array[Byte] = {
     val arr = new Array[Byte](n)
     read(arr, 0, n)
     arr
   }
 
-  def skipByte(): Unit = {
+  override def skipByte(): Unit = {
     ensure(1)
     off += 1
   }
 
-  def skipInt(): Unit = {
+  override def skipInt(): Unit = {
     ensure(4)
     off += 4
   }
 
-  def skipLong(): Unit = {
+  override def skipLong(): Unit = {
     ensure(8)
     off += 8
   }
 
-  def skipFloat(): Unit = {
+  override def skipFloat(): Unit = {
     ensure(4)
     off += 4
   }
 
-  def skipDouble(): Unit = {
+  override def skipDouble(): Unit = {
     ensure(8)
     off += 8
   }
 
-  def skipBytes(n0: Int): Unit = {
+  override def skipBytes(n0: Int): Unit = {
     var n = n0
     if (off + n > end) {
       n -= (end - off)
@@ -488,7 +491,7 @@ final class BlockingInputBuffer(blockSize: Int, in: InputBlockBuffer) extends In
     }
   }
 
-  def readDoubles(to: Array[Double], toOff0: Int, n0: Int): Unit = {
+  override def readDoubles(to: Array[Double], toOff0: Int, n0: Int): Unit = {
     assert(toOff0 >= 0)
     assert(n0 >= 0)
     assert(toOff0 <= to.length - n0)
@@ -513,13 +516,14 @@ final class BlockingInputBuffer(blockSize: Int, in: InputBlockBuffer) extends In
 final class StreamBlockInputBuffer(in: InputStream) extends InputBlockBuffer {
   private[this] val lenBuf = new Array[Byte](4)
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
   // this takes a virtual offset and will seek the underlying stream to offset >> 16
-  def seek(offset: Long): Unit = in.asInstanceOf[ByteTrackingInputStream].seek(offset >> 16)
+  override def seek(offset: Long): Unit =
+    in.asInstanceOf[ByteTrackingInputStream].seek(offset >> 16)
 
-  def readBlock(buf: Array[Byte]): Int = {
+  override def readBlock(buf: Array[Byte]): Int = {
     in.readFully(lenBuf, 0, 4)
     val len = Memory.loadInt(lenBuf, 0)
     assert(len >= 0)
@@ -533,10 +537,10 @@ final class LZ4InputBlockBuffer(lz4: LZ4, blockSize: Int, in: InputBlockBuffer)
     extends InputBlockBuffer {
   private[this] val comp = new Array[Byte](4 + lz4.maxCompressedLength(blockSize))
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 
   override def skipBytesReadRemainder(n0: Int, buf: Array[Byte]): Int = {
     var n = n0
@@ -557,7 +561,7 @@ final class LZ4InputBlockBuffer(lz4: LZ4, blockSize: Int, in: InputBlockBuffer)
     return -n
   }
 
-  def readBlock(buf: Array[Byte]): Int = {
+  override def readBlock(buf: Array[Byte]): Int = {
     val blockLen = in.readBlock(comp)
     val result = if (blockLen == -1) {
       -1
@@ -576,12 +580,12 @@ final class LZ4SizeBasedCompressingInputBlockBuffer(lz4: LZ4, blockSize: Int, in
   private[this] val comp = new Array[Byte](8 + lz4.maxCompressedLength(blockSize))
   private[this] var lim = 0
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 
-  def readBlock(buf: Array[Byte]): Int = {
+  override def readBlock(buf: Array[Byte]): Int = {
     val blockLen = in.readBlock(comp)
     val result = if (blockLen == -1) {
       -1
@@ -606,7 +610,7 @@ final class LZ4SizeBasedCompressingInputBlockBuffer(lz4: LZ4, blockSize: Int, in
 
 object ZstdDecompressLib {
   val instance = ThreadLocal.withInitial(new Supplier[ZstdDecompressCtx]() {
-    def get: ZstdDecompressCtx = new ZstdDecompressCtx()
+    override def get: ZstdDecompressCtx = new ZstdDecompressCtx()
   })
 }
 
@@ -614,12 +618,12 @@ final class ZstdInputBlockBuffer(blockSize: Int, in: InputBlockBuffer) extends I
   private[this] val zstd = ZstdDecompressLib.instance.get
   private[this] val comp = new Array[Byte](4 + Zstd.compressBound(blockSize.toLong).toInt)
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 
-  def readBlock(buf: Array[Byte]): Int = {
+  override def readBlock(buf: Array[Byte]): Int = {
     val blockLen = in.readBlock(comp)
     if (blockLen == -1) {
       blockLen
@@ -637,12 +641,12 @@ final class ZstdSizedBasedInputBlockBuffer(blockSize: Int, in: InputBlockBuffer)
   private[this] val zstd = ZstdDecompressLib.instance.get
   private[this] val comp = new Array[Byte](4 + Zstd.compressBound(blockSize.toLong).toInt)
 
-  def close(): Unit =
+  override def close(): Unit =
     in.close()
 
-  def seek(offset: Long): Unit = in.seek(offset)
+  override def seek(offset: Long): Unit = in.seek(offset)
 
-  def readBlock(buf: Array[Byte]): Int = {
+  override def readBlock(buf: Array[Byte]): Int = {
     val blockLen = in.readBlock(comp)
     if (blockLen == -1) {
       blockLen
diff --git a/hail/hail/src/is/hail/io/OutputBuffers.scala b/hail/hail/src/is/hail/io/OutputBuffers.scala
index 876e34fd4fa..0f0fc39e3a0 100644
--- a/hail/hail/src/is/hail/io/OutputBuffers.scala
+++ b/hail/hail/src/is/hail/io/OutputBuffers.scala
@@ -2,8 +2,7 @@ package is.hail.io
 
 import is.hail.annotations.{Memory, Region}
 import is.hail.io.compress.LZ4
-import is.hail.utils._
-import is.hail.utils.richUtils.ByteTrackingOutputStream
+import is.hail.utils.implicits.{toRichBoolean, ByteTrackingOutputStream}
 
 import java.io._
 import java.util.function.Supplier
@@ -13,7 +12,7 @@ import com.github.luben.zstd.{Zstd, ZstdCompressCtx}
 trait OutputBuffer extends Closeable {
   def flush(): Unit
 
-  def close(): Unit
+  override def close(): Unit
 
   def indexOffset(): Long
 
@@ -64,7 +63,7 @@ final class StreamOutputBuffer(out: OutputStream) extends OutputBuffer {
 
   override def close(): Unit = out.close()
 
-  def indexOffset(): Long = out.asInstanceOf[ByteTrackingOutputStream].bytesWritten
+  override def indexOffset(): Long = out.asInstanceOf[ByteTrackingOutputStream].bytesWritten
 
   override def writeByte(b: Byte): Unit = out.write(b.toInt)
 
@@ -73,28 +72,28 @@ final class StreamOutputBuffer(out: OutputStream) extends OutputBuffer {
     out.write(buf, 0, 4)
   }
 
-  def writeLong(l: Long): Unit = {
+  override def writeLong(l: Long): Unit = {
     Memory.storeLong(buf, 0, l)
     out.write(buf, 0, 8)
   }
 
-  def writeFloat(f: Float): Unit = {
+  override def writeFloat(f: Float): Unit = {
     Memory.storeFloat(buf, 0, f)
     out.write(buf, 0, 4)
   }
 
-  def writeDouble(d: Double): Unit = {
+  override def writeDouble(d: Double): Unit = {
     Memory.storeDouble(buf, 0, d)
     out.write(buf, 0, 8)
   }
 
-  def writeBytes(region: Region, off: Long, n: Int): Unit =
+  override def writeBytes(region: Region, off: Long, n: Int): Unit =
     out.write(Region.loadBytes(off, n))
 
-  def writeBytes(addr: Long, n: Int): Unit =
+  override def writeBytes(addr: Long, n: Int): Unit =
     out.write(Region.loadBytes(addr, n))
 
-  def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit = {
+  override def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit = {
     var i = 0
     while (i < n) {
       writeDouble(from(fromOff + i))
@@ -104,40 +103,40 @@ final class StreamOutputBuffer(out: OutputStream) extends OutputBuffer {
 }
 
 final class MemoryOutputBuffer(mb: MemoryBuffer) extends OutputBuffer {
-  def flush(): Unit = {}
+  override def flush(): Unit = {}
 
-  def close(): Unit = {}
+  override def close(): Unit = {}
 
-  def indexOffset(): Long = ???
+  override def indexOffset(): Long = ???
 
-  def writeByte(b: Byte): Unit = mb.writeByte(b)
+  override def writeByte(b: Byte): Unit = mb.writeByte(b)
 
-  def writeInt(i: Int): Unit = mb.writeInt(i)
+  override def writeInt(i: Int): Unit = mb.writeInt(i)
 
-  def writeLong(l: Long): Unit = mb.writeLong(l)
+  override def writeLong(l: Long): Unit = mb.writeLong(l)
 
-  def writeFloat(f: Float): Unit = mb.writeFloat(f)
+  override def writeFloat(f: Float): Unit = mb.writeFloat(f)
 
-  def writeDouble(d: Double): Unit = mb.writeDouble(d)
+  override def writeDouble(d: Double): Unit = mb.writeDouble(d)
 
-  def writeBytes(region: Region, off: Long, n: Int): Unit = mb.writeBytes(off, n)
+  override def writeBytes(region: Region, off: Long, n: Int): Unit = mb.writeBytes(off, n)
 
-  def writeBytes(addr: Long, n: Int): Unit = mb.writeBytes(addr, n)
+  override def writeBytes(addr: Long, n: Int): Unit = mb.writeBytes(addr, n)
 
-  def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit = ???
+  override def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit = ???
 }
 
 final class LEB128OutputBuffer(out: OutputBuffer) extends OutputBuffer {
-  def flush(): Unit = out.flush()
+  override def flush(): Unit = out.flush()
 
-  def close(): Unit =
+  override def close(): Unit =
     out.close()
 
-  def indexOffset(): Long = out.indexOffset()
+  override def indexOffset(): Long = out.indexOffset()
 
-  def writeByte(b: Byte): Unit = out.writeByte(b)
+  override def writeByte(b: Byte): Unit = out.writeByte(b)
 
-  def writeInt(i: Int): Unit = {
+  override def writeInt(i: Int): Unit = {
     var j = i
     do {
       var b = j & 0x7f
@@ -148,7 +147,7 @@ final class LEB128OutputBuffer(out: OutputBuffer) extends OutputBuffer {
     } while (j != 0)
   }
 
-  def writeLong(l: Long): Unit = {
+  override def writeLong(l: Long): Unit = {
     var j = l
     do {
       var b = j & 0x7f
@@ -159,15 +158,15 @@ final class LEB128OutputBuffer(out: OutputBuffer) extends OutputBuffer {
     } while (j != 0)
   }
 
-  def writeFloat(f: Float): Unit = out.writeFloat(f)
+  override def writeFloat(f: Float): Unit = out.writeFloat(f)
 
-  def writeDouble(d: Double): Unit = out.writeDouble(d)
+  override def writeDouble(d: Double): Unit = out.writeDouble(d)
 
-  def writeBytes(region: Region, off: Long, n: Int): Unit = out.writeBytes(region, off, n)
+  override def writeBytes(region: Region, off: Long, n: Int): Unit = out.writeBytes(region, off, n)
 
-  def writeBytes(addr: Long, n: Int): Unit = out.writeBytes(addr, n)
+  override def writeBytes(addr: Long, n: Int): Unit = out.writeBytes(addr, n)
 
-  def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit =
+  override def writeDoubles(from: Array[Double], fromOff: Int, n: Int): Unit =
     out.writeDoubles(from, fromOff, n)
 }
 
@@ -175,7 +174,7 @@ final class BlockingOutputBuffer(blockSize: Int, out: OutputBlockBuffer) extends
   private val buf: Array[Byte] = new Array[Byte](blockSize)
   private var off: Int = 0
 
-  def indexOffset(): Long = {
+  override def indexOffset(): Long = {
     if (off == blockSize)
       writeBlock()
     (out.getPos() << 16) | off
@@ -186,54 +185,54 @@ final class BlockingOutputBuffer(blockSize: Int, out: OutputBlockBuffer) extends
     off = 0
   }
 
-  def flush(): Unit = {
+  override def flush(): Unit = {
     writeBlock()
     out.flush()
   }
 
-  def close(): Unit = {
+  override def close(): Unit = {
     flush()
     out.close()
   }
 
-  def writeByte(b: Byte): Unit = {
+  override def writeByte(b: Byte): Unit = {
     if (off + 1 > buf.length)
       writeBlock()
     Memory.storeByte(buf, off.toLong, b)
     off += 1
   }
 
-  def writeInt(i: Int): Unit = {
+  override def writeInt(i: Int): Unit = {
     if (off + 4 > buf.length)
       writeBlock()
     Memory.storeInt(buf, off.toLong, i)
     off += 4
   }
 
-  def writeLong(l: Long): Unit = {
+  override def writeLong(l: Long): Unit = {
     if (off + 8 > buf.length)
       writeBlock()
     Memory.storeLong(buf, off.toLong, l)
     off += 8
   }
 
-  def writeFloat(f: Float): Unit = {
+  override def writeFloat(f: Float): Unit = {
     if (off + 4 > buf.length)
       writeBlock()
     Memory.storeFloat(buf, off.toLong, f)
     off += 4
   }
 
-  def writeDouble(d: Double): Unit = {
+  override def writeDouble(d: Double): Unit = {
     if (off + 8 > buf.length)
       writeBlock()
     Memory.storeDouble(buf, off.toLong, d)
     off += 8
   }
 
-  def writeBytes(fromRegion: Region, fromOff0: Long, n0: Int) = writeBytes(fromOff0, n0)
+  override def writeBytes(fromRegion: Region, fromOff0: Long, n0: Int) = writeBytes(fromOff0, n0)
 
-  def writeBytes(addr0: Long, n0: Int): Unit = {
+  override def writeBytes(addr0: Long, n0: Int): Unit = {
     assert(n0 >= 0)
     var addr = addr0
     var n = n0
@@ -251,7 +250,7 @@ final class BlockingOutputBuffer(blockSize: Int, out: OutputBlockBuffer) extends
     off += n
   }
 
-  def writeDoubles(from: Array[Double], fromOff0: Int, n0: Int): Unit = {
+  override def writeDoubles(from: Array[Double], fromOff0: Int, n0: Int): Unit = {
     assert(n0 >= 0)
     assert(fromOff0 >= 0)
     assert(fromOff0 <= from.length - n0)
@@ -274,38 +273,38 @@ final class BlockingOutputBuffer(blockSize: Int, out: OutputBlockBuffer) extends
 final class StreamBlockOutputBuffer(out: OutputStream) extends OutputBlockBuffer {
   private val lenBuf = new Array[Byte](4)
 
-  def flush(): Unit =
+  override def flush(): Unit =
     out.flush()
 
-  def close(): Unit =
+  override def close(): Unit =
     out.close()
 
-  def writeBlock(buf: Array[Byte], len: Int): Unit = {
+  override def writeBlock(buf: Array[Byte], len: Int): Unit = {
     Memory.storeInt(lenBuf, 0, len)
     out.write(lenBuf, 0, 4)
     out.write(buf, 0, len)
   }
 
-  def getPos(): Long = out.asInstanceOf[ByteTrackingOutputStream].bytesWritten
+  override def getPos(): Long = out.asInstanceOf[ByteTrackingOutputStream].bytesWritten
 }
 
 final class LZ4OutputBlockBuffer(lz4: LZ4, blockSize: Int, out: OutputBlockBuffer)
     extends OutputBlockBuffer {
   private val comp = new Array[Byte](4 + lz4.maxCompressedLength(blockSize))
 
-  def flush(): Unit =
+  override def flush(): Unit =
     out.flush()
 
-  def close(): Unit =
+  override def close(): Unit =
     out.close()
 
-  def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
+  override def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
     val compLen = lz4.compress(comp, 4, buf, decompLen)
     Memory.storeInt(comp, 0, decompLen) // decompLen
     out.writeBlock(comp, compLen + 4)
   }
 
-  def getPos(): Long = out.getPos()
+  override def getPos(): Long = out.getPos()
 }
 
 final class LZ4SizeBasedCompressingOutputBlockBuffer(
@@ -316,13 +315,13 @@ final class LZ4SizeBasedCompressingOutputBlockBuffer(
 ) extends OutputBlockBuffer {
   private val comp = new Array[Byte](8 + lz4.maxCompressedLength(blockSize))
 
-  def flush(): Unit =
+  override def flush(): Unit =
     out.flush()
 
-  def close(): Unit =
+  override def close(): Unit =
     out.close()
 
-  def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
+  override def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
     if (decompLen < minCompressionSize) {
       System.arraycopy(buf, 0, comp, 4, decompLen)
       Memory.storeInt(comp, 0, 0) // uncompressed
@@ -335,12 +334,12 @@ final class LZ4SizeBasedCompressingOutputBlockBuffer(
     }
   }
 
-  def getPos(): Long = out.getPos()
+  override def getPos(): Long = out.getPos()
 }
 
 object ZstdCompressLib {
   val instance = ThreadLocal.withInitial(new Supplier[ZstdCompressCtx]() {
-    def get = {
+    override def get = {
       val zstd = new ZstdCompressCtx()
       zstd.setLevel(Zstd.defaultCompressionLevel())
       zstd.setChecksum(false)
@@ -354,17 +353,17 @@ final class ZstdOutputBlockBuffer(blockSize: Int, out: OutputBlockBuffer)
   private[this] val zstd = ZstdCompressLib.instance.get
   private[this] val comp = new Array[Byte](4 + Zstd.compressBound(blockSize.toLong).toInt)
 
-  def flush(): Unit = out.flush()
+  override def flush(): Unit = out.flush()
 
-  def close(): Unit = out.close()
+  override def close(): Unit = out.close()
 
-  def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
+  override def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
     val compLen = zstd.compressByteArray(comp, 4, comp.length - 4, buf, 0, decompLen)
     Memory.storeInt(comp, 0, decompLen.toInt)
     out.writeBlock(comp, compLen.toInt + 4)
   }
 
-  def getPos(): Long = out.getPos()
+  override def getPos(): Long = out.getPos()
 }
 
 final class ZstdSizedBasedOutputBlockBuffer(
@@ -375,11 +374,11 @@ final class ZstdSizedBasedOutputBlockBuffer(
   private[this] val zstd = ZstdCompressLib.instance.get
   private[this] val comp = new Array[Byte](4 + Zstd.compressBound(blockSize.toLong).toInt)
 
-  def flush(): Unit = out.flush()
+  override def flush(): Unit = out.flush()
 
-  def close(): Unit = out.close()
+  override def close(): Unit = out.close()
 
-  def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
+  override def writeBlock(buf: Array[Byte], decompLen: Int): Unit = {
     val compLen = if (decompLen < minCompressionSize) {
       System.arraycopy(buf, 0, comp, 4, decompLen)
       Memory.storeInt(comp, 0, 0)
@@ -393,5 +392,5 @@ final class ZstdSizedBasedOutputBlockBuffer(
     out.writeBlock(comp, compLen + 4)
   }
 
-  def getPos(): Long = out.getPos()
+  override def getPos(): Long = out.getPos()
 }
diff --git a/hail/hail/src/is/hail/io/TypedCodecSpec.scala b/hail/hail/src/is/hail/io/TypedCodecSpec.scala
index 87fdc32c573..16e6b1faf32 100644
--- a/hail/hail/src/is/hail/io/TypedCodecSpec.scala
+++ b/hail/hail/src/is/hail/io/TypedCodecSpec.scala
@@ -17,19 +17,20 @@ object TypedCodecSpec {
 
 final case class TypedCodecSpec(_eType: EType, _vType: Type, _bufferSpec: BufferSpec)
     extends AbstractTypedCodecSpec {
-  def encodedType: EType = _eType
-  def encodedVirtualType: Type = _vType
+  override def encodedType: EType = _eType
+  override def encodedVirtualType: Type = _vType
 
-  def buildEncoder(ctx: ExecuteContext, t: PType): (OutputStream, HailClassLoader) => Encoder = {
+  override def buildEncoder(ctx: ExecuteContext, t: PType)
+    : (OutputStream, HailClassLoader) => Encoder = {
     val bufferToEncoder = encodedType.buildEncoder(ctx, t)
     (out: OutputStream, theHailClassLoader: HailClassLoader) =>
       bufferToEncoder(_bufferSpec.buildOutputBuffer(out), theHailClassLoader)
   }
 
-  def decodedPType(requestedType: Type): PType =
+  override def decodedPType(requestedType: Type): PType =
     encodedType.decodedPType(requestedType)
 
-  def buildDecoder(ctx: ExecuteContext, requestedType: Type)
+  override def buildDecoder(ctx: ExecuteContext, requestedType: Type)
     : (PType, (InputStream, HailClassLoader) => Decoder) = {
     val (rt, bufferToDecoder) = encodedType.buildDecoder(ctx, requestedType)
     (
@@ -45,9 +46,9 @@ final case class TypedCodecSpec(_eType: EType, _vType: Type, _bufferSpec: Buffer
     pType -> makeDec
   }
 
-  def buildCodeInputBuffer(is: Code[InputStream]): Code[InputBuffer] =
+  override def buildCodeInputBuffer(is: Code[InputStream]): Code[InputBuffer] =
     _bufferSpec.buildCodeInputBuffer(is)
 
-  def buildCodeOutputBuffer(os: Code[OutputStream]): Code[OutputBuffer] =
+  override def buildCodeOutputBuffer(os: Code[OutputStream]): Code[OutputBuffer] =
     _bufferSpec.buildCodeOutputBuffer(os)
 }
diff --git a/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala b/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala
index 4d3de648d5c..e77218b62c1 100644
--- a/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala
+++ b/hail/hail/src/is/hail/io/avro/AvroPartitionReader.scala
@@ -3,6 +3,7 @@ package is.hail.io.avro
 import is.hail.annotations.Region
 import is.hail.asm4s.{Field => _, _}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder, EmitMethodBuilder, EmitValue, IEmitCode}
 import is.hail.expr.ir.defs.PartitionReader
 import is.hail.expr.ir.streams.StreamProducer
@@ -11,8 +12,6 @@ import is.hail.types.physical.{PCanonicalTuple, PInt64Required}
 import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces.{primitive, SBaseStructValue, SStreamValue}
 import is.hail.types.virtual._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.jdk.CollectionConverters._
 
@@ -25,7 +24,7 @@ import org.apache.avro.io.DatumReader
 import org.json4s.{Extraction, JValue}
 
 case class AvroPartitionReader(schema: Schema, uidFieldName: String) extends PartitionReader {
-  def contextType: Type = TStruct("partitionPath" -> TString, "partitionIndex" -> TInt64)
+  override def contextType: Type = TStruct("partitionPath" -> TString, "partitionIndex" -> TInt64)
 
   def fullRowTypeWithoutUIDs: TStruct = AvroReader.schemaToType(schema)
 
@@ -78,7 +77,7 @@ case class AvroPartitionReader(schema: Schema, uidFieldName: String) extends Par
         override def method: EmitMethodBuilder[_] = cb.emb
         val length: Option[EmitCodeBuilder => Code[Int]] = None
 
-        def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
+        override def initialize(cb: EmitCodeBuilder, outerRegion: Value[Region]): Unit = {
           val mb = cb.emb
           val codeSchema = cb.newLocal("schema", mb.getObject(schema))
           cb.assign(record, Code.newInstance[GenericData.Record, Schema](codeSchema))
@@ -121,14 +120,14 @@ case class AvroPartitionReader(schema: Schema, uidFieldName: String) extends Par
           }
         }
 
-        def close(cb: EmitCodeBuilder): Unit = cb += it.invoke[Unit]("close")
+        override def close(cb: EmitCodeBuilder): Unit = cb += it.invoke[Unit]("close")
       }
 
       SStreamValue(producer)
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
 
 object AvroReader {
diff --git a/hail/hail/src/is/hail/io/avro/AvroTableReader.scala b/hail/hail/src/is/hail/io/avro/AvroTableReader.scala
index f82b1dacc8f..fd6b7bef20b 100644
--- a/hail/hail/src/is/hail/io/avro/AvroTableReader.scala
+++ b/hail/hail/src/is/hail/io/avro/AvroTableReader.scala
@@ -1,6 +1,7 @@
 package is.hail.io.avro
 
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs.{
   ArrayZipBehavior, Cast, I32, Literal, MakeStruct, PartitionReader, ReadPartition, StreamIota,
@@ -11,7 +12,7 @@ import is.hail.rvd.RVDPartitioner
 import is.hail.types.VirtualTypeWithReq
 import is.hail.types.physical.{PCanonicalStruct, PCanonicalTuple, PInt64Required}
 import is.hail.types.virtual._
-import is.hail.utils.{plural, FastSeq}
+import is.hail.utils.plural
 
 import org.json4s.{Formats, JValue}
 
@@ -39,9 +40,9 @@ class AvroTableReader(
       RVDPartitioner.unkeyed(stateManager, paths.length)
     }
 
-  def pathsUsed: Seq[String] = paths
+  override def pathsUsed: Seq[String] = paths
 
-  def partitionCounts: Option[IndexedSeq[Long]] = None
+  override def partitionCounts: Option[IndexedSeq[Long]] = None
 
   override def uidType = TTuple(TInt64, TInt64)
 
@@ -66,7 +67,7 @@ class AvroTableReader(
     : VirtualTypeWithReq =
     VirtualTypeWithReq(PCanonicalStruct(required = true))
 
-  def renderShort(): String = defaultRender()
+  override def renderShort(): String = defaultRender()
 
   override def lower(ctx: ExecuteContext, requestedType: TableType): TableStage = {
     val globals = MakeStruct(FastSeq())
diff --git a/hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala b/hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala
index c98b05d4bd2..88c8711765e 100644
--- a/hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala
+++ b/hail/hail/src/is/hail/io/bgen/BgenRDDPartitions.scala
@@ -1,9 +1,9 @@
 package is.hail.io.bgen
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 
diff --git a/hail/hail/src/is/hail/io/bgen/BgenSettings.scala b/hail/hail/src/is/hail/io/bgen/BgenSettings.scala
index c22a2fea6de..63c41c8c968 100644
--- a/hail/hail/src/is/hail/io/bgen/BgenSettings.scala
+++ b/hail/hail/src/is/hail/io/bgen/BgenSettings.scala
@@ -1,5 +1,6 @@
 package is.hail.io.bgen
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.PruneDeadFields
 import is.hail.io._
 import is.hail.rvd.AbstractIndexSpec
@@ -115,7 +116,7 @@ object BgenSettings {
     ))
 
     new AbstractIndexSpec {
-      def relPath = fatal("relPath called for bgen index spec")
+      override def relPath = fatal("relPath called for bgen index spec")
       val leafCodec = TypedCodecSpec(leafEType, leafVType, bufferSpec)
       val internalNodeCodec = TypedCodecSpec(internalNodeEType, internalNodeVType, bufferSpec)
       val keyType = keyVType
diff --git a/hail/hail/src/is/hail/io/bgen/LoadBgen.scala b/hail/hail/src/is/hail/io/bgen/LoadBgen.scala
index 90fda6bff12..ed1b563693c 100644
--- a/hail/hail/src/is/hail/io/bgen/LoadBgen.scala
+++ b/hail/hail/src/is/hail/io/bgen/LoadBgen.scala
@@ -2,7 +2,11 @@ package is.hail.io.bgen
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{
   EmitCode, EmitCodeBuilder, EmitMethodBuilder, EmitSettable, EmitValue, IEmitCode, IR,
   LowerMatrixIR, MatrixHybridReader, MatrixReader, PartitionNativeIntervalReader, TableNativeReader,
@@ -22,7 +26,6 @@ import is.hail.types.physical.stypes.concrete.{SJavaArrayString, SStackStruct}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 import scala.io.Source
@@ -156,6 +159,9 @@ object LoadBgen extends Logging {
       )
   }
 
+  private[this] lazy val EntryPattern =
+    ".*part-[0-9]+(-[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})?".r.pattern
+
   def getAllFileListEntries(fs: FS, files: Array[String]): Array[FileListEntry] = {
     val badFiles = ArraySeq.newBuilder[String]
 
@@ -172,9 +178,7 @@ object LoadBgen extends Logging {
         if (fileListEntry.isDirectory)
           fs.listDirectory(file)
             .filter(fileListEntry =>
-              ".*part-[0-9]+(-[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})?".r.matches(
-                fileListEntry.getPath
-              )
+              EntryPattern.matcher(fileListEntry.getPath).matches()
             )
         else
           Array(fileListEntry)
@@ -192,9 +196,6 @@ object LoadBgen extends Logging {
     fileListEntries
   }
 
-  def getAllFilePaths(fs: FS, files: Array[String]): Array[String] =
-    getAllFileListEntries(fs, files).map(_.getPath.toString)
-
   def getBgenFileMetadata(
     ctx: ExecuteContext,
     files: Array[FileListEntry],
@@ -512,19 +513,19 @@ class MatrixBGENReader(
   filePartitionInfo: IndexedSeq[FilePartitionInfo],
   variants: Option[String],
 ) extends MatrixHybridReader {
-  def pathsUsed: Seq[String] = filePartitionInfo.map(_.metadata.path)
+  override def pathsUsed: Seq[String] = filePartitionInfo.map(_.metadata.path)
 
   lazy val nVariants: Long = filePartitionInfo.map(_.metadata.nVariants).sum
 
-  def rowUIDType = TTuple(TInt64, TInt64)
+  override def rowUIDType = TTuple(TInt64, TInt64)
 
-  def colUIDType = TInt64
+  override def colUIDType = TInt64
 
   private val nSamples = sampleIds.length
 
-  def columnCount: Option[Int] = Some(nSamples)
+  override def columnCount: Option[Int] = Some(nSamples)
 
-  def partitionCounts: Option[IndexedSeq[Long]] = None
+  override def partitionCounts: Option[IndexedSeq[Long]] = None
 
   private var _settings: BgenSettings = _
 
@@ -576,7 +577,7 @@ class MatrixBGENReader(
 
   override def toJValue: JValue = params.toJValue
 
-  def renderShort(): String = defaultRender()
+  override def renderShort(): String = defaultRender()
 
   override def hashCode(): Int = params.hashCode()
 
@@ -674,12 +675,12 @@ case class BgenPartitionReaderWithVariantFilter(
   lazy val uidType = TTuple(TInt64, TInt64)
   lazy val fullRowType: TStruct = MatrixBGENReader.fullTableType(rg).rowType
 
-  def rowRequiredness(requestedType: TStruct): RStruct =
+  override def rowRequiredness(requestedType: TStruct): RStruct =
     StagedBGENReader.rowRequiredness(requestedType)
 
-  def uidFieldName: String = TableReader.uidFieldName
+  override def uidFieldName: String = TableReader.uidFieldName
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -832,7 +833,7 @@ case class BgenPartitionReaderWithVariantFilter(
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
 
 case class BgenPartitionReader(fileMetadata: Array[BgenFileMetadata], rg: Option[String])
@@ -848,12 +849,12 @@ case class BgenPartitionReader(fileMetadata: Array[BgenFileMetadata], rg: Option
 
   lazy val fullRowType: TStruct = MatrixBGENReader.fullTableType(rg).rowType
 
-  def rowRequiredness(requestedType: TStruct): RStruct =
+  override def rowRequiredness(requestedType: TStruct): RStruct =
     StagedBGENReader.rowRequiredness(requestedType)
 
-  def uidFieldName: String = TableReader.uidFieldName
+  override def uidFieldName: String = TableReader.uidFieldName
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
@@ -975,5 +976,5 @@ case class BgenPartitionReader(fileMetadata: Array[BgenFileMetadata], rg: Option
     }
   }
 
-  def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
+  override def toJValue: JValue = Extraction.decompose(this)(PartitionReader.formats)
 }
diff --git a/hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala b/hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala
index 2b42b0f9d7c..e45bcfe8d30 100644
--- a/hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala
+++ b/hail/hail/src/is/hail/io/bgen/StagedBGENReader.scala
@@ -3,6 +3,8 @@ package is.hail.io.bgen
 import is.hail.annotations.Region
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.{
   uuid4, ArraySorter, EmitCode, EmitCodeBuilder, EmitFunctionBuilder, EmitSettable, IEmitCode,
   LowerMatrixIR, ParamType, StagedArrayBuilder,
@@ -21,8 +23,7 @@ import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces.{primitive, NoBoxLongIterator, SBaseStructValue}
 import is.hail.types.physical.stypes.primitives.SInt64
 import is.hail.types.virtual._
-import is.hail.utils.{CompressionUtils, FastSeq}
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.utils.CompressionUtils
 import is.hail.variant.Call2
 
 import org.objectweb.asm.Opcodes._
@@ -619,7 +620,7 @@ object BGENFunctions extends RegistryFunctions {
       Array(TVariable("locusType")),
     ) {
       case (
-            er,
+            r,
             cb,
             Seq(locType),
             _,
@@ -634,7 +635,7 @@ object BGENFunctions extends RegistryFunctions {
         val path = _path.asString.loadString(cb)
         val idxPath = _idxPath.asString.loadString(cb)
         val recoding =
-          cb.memoize(coerce[Map[String, String]](svalueToJavaValue(cb, er.region, _recoding)))
+          cb.memoize(coerce[Map[String, String]](svalueToJavaValue(cb, r, _recoding)))
         val skipInvalidLoci = _skipInvalidLoci.asBoolean.value
         val bufferSize = _bufferSize.asInt.value
 
@@ -712,11 +713,11 @@ object BGENFunctions extends RegistryFunctions {
           BufferSpec.wireSpec,
         )
 
-        def dumpBuffer(cb: EmitCodeBuilder) = {
-          val sorter = new ArraySorter(er, buffer)
+        def dumpBuffer() = {
+          val sorter = new ArraySorter(cb.emb, r, buffer)
           sorter.sort(
             cb,
-            er.region,
+            r,
             { case (cb, _, l, r) =>
               val lv = bufferSct.loadToSValue(cb, l).asBaseStruct.subset("locus", "alleles")
               val rv = bufferSct.loadToSValue(cb, r).asBaseStruct.subset("locus", "alleles")
@@ -757,7 +758,7 @@ object BGENFunctions extends RegistryFunctions {
           nRead < nVariants, {
             StagedBGENReader.decodeRow(
               cb,
-              er.region,
+              r,
               cbfis,
               nSamples,
               fileIdx,
@@ -771,8 +772,8 @@ object BGENFunctions extends RegistryFunctions {
                 // do nothing if missing (invalid locus)
               },
               { case row: SBaseStructValue =>
-                cb.if_(currSize ceq bufferSize, dumpBuffer(cb))
-                buffer.add(cb, bufferSct.coerceSCode(cb, row, er.region, false).code)
+                cb.if_(currSize ceq bufferSize, dumpBuffer())
+                buffer.add(cb, bufferSct.coerceSCode(cb, row, r, false).code)
                 cb.assign(currSize, currSize + 1)
                 cb.assign(nWritten, nWritten + 1)
               },
@@ -780,7 +781,7 @@ object BGENFunctions extends RegistryFunctions {
             cb.assign(nRead, nRead + 1)
           },
         )
-        cb.if_(currSize > 0, dumpBuffer(cb))
+        cb.if_(currSize > 0, dumpBuffer())
 
         val ecb = cb.emb.genEmitClass[Unit]("buffer_stream")
         ecb.cb.addInterface(typeInfo[NoBoxLongIterator].iname)
@@ -906,7 +907,7 @@ object BGENFunctions extends RegistryFunctions {
         )
 
         val nAdded = cb.newLocal[Long]("nAdded", 0)
-        mergedStream.memoryManagedConsume(er.region, cb) { cb =>
+        mergedStream.memoryManagedConsume(r, cb) { cb =>
           val row = mergedStream.element.toI(cb).getOrAssert(cb).asBaseStruct
           val key = row.subset("locus", "alleles")
           val offset = row.loadField(cb, "offset").getOrAssert(cb).asInt64.value
@@ -915,7 +916,7 @@ object BGENFunctions extends RegistryFunctions {
             cb,
             IEmitCode.present(cb, key),
             offset,
-            IEmitCode.present(cb, SStackStruct.constructFromArgs(cb, er.region, TStruct())),
+            IEmitCode.present(cb, SStackStruct.constructFromArgs(cb, r, TStruct())),
           )
         }
         cb.if_(
diff --git a/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala b/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala
index 046171318bd..3bf3efebc7c 100644
--- a/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala
+++ b/hail/hail/src/is/hail/io/fs/AzureStorageFS.scala
@@ -151,9 +151,9 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
       case _: IllegalArgumentException => false
     }
 
-  def getConfiguration(): Unit = ()
+  override def getConfiguration(): Unit = ()
 
-  def setConfiguration(config: Any): Unit = {}
+  override def setConfiguration(config: Any): Unit = {}
 
   // ABS errors if you attempt credentialed access for a public container,
   // so we try once with credentials, if that fails use anonymous access for
@@ -190,7 +190,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
     getServiceClient(url).getBlobContainerClient(url.container)
   }
 
-  def openNoCompression(url: URL): SeekableDataInputStream = handlePublicAccessError(url) {
+  override def openNoCompression(url: URL): SeekableDataInputStream = handlePublicAccessError(url) {
     val blobSize = getBlobClient(url).getProperties.getBlobSize
 
     val is: SeekableInputStream = new FSSeekableInputStream {
@@ -238,7 +238,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
     new WrappedSeekableDataInputStream(is)
   }
 
-  def createNoCompression(url: URL): PositionedDataOutputStream = retryTransientErrors {
+  override def createNoCompression(url: URL): PositionedDataOutputStream = retryTransientErrors {
     val blockBlobClient = getBlobClient(url).getBlockBlobClient
 
     val os: PositionedOutputStream = new FSPositionedOutputStream(4 * 1024 * 1024) {
@@ -268,7 +268,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
     new WrappedPositionedDataOutputStream(os)
   }
 
-  def delete(url: URL, recursive: Boolean): Unit = retryTransientErrors {
+  override def delete(url: URL, recursive: Boolean): Unit = retryTransientErrors {
     val blobClient: BlobClient = getBlobClient(url)
 
     if (recursive) {
@@ -294,7 +294,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
     }
   }
 
-  def listDirectory(url: URL): Array[FileListEntry] = handlePublicAccessError(url) {
+  override def listDirectory(url: URL): Array[FileListEntry] = handlePublicAccessError(url) {
     val blobContainerClient: BlobContainerClient = getContainerClient(url)
     val statList: ArrayBuffer[FileListEntry] = ArrayBuffer()
 
@@ -307,7 +307,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
     statList.toArray
   }
 
-  def glob(url: URL): Array[FileListEntry] = handlePublicAccessError(url) {
+  override def glob(url: URL): Array[FileListEntry] = handlePublicAccessError(url) {
     globWithPrefix(prefix = url.withPath(""), path = dropTrailingSlash(url.path))
   }
 
@@ -351,7 +351,7 @@ class AzureStorageFS(val credential: AzureCloudCredentials) extends FS {
       Some(getBlobClient(url).getProperties.getETag)
     }
 
-  def makeQualified(filename: String): String = {
+  override def makeQualified(filename: String): String = {
     parseUrl(filename): Unit
     filename
   }
diff --git a/hail/hail/src/is/hail/io/fs/FS.scala b/hail/hail/src/is/hail/io/fs/FS.scala
index fa1ff6871c8..ffa6e92bb4d 100644
--- a/hail/hail/src/is/hail/io/fs/FS.scala
+++ b/hail/hail/src/is/hail/io/fs/FS.scala
@@ -18,14 +18,14 @@ import org.apache.hadoop
 
 class WrappedSeekableDataInputStream(is: SeekableInputStream)
     extends DataInputStream(is) with Seekable {
-  def getPosition: Long = is.getPosition
+  override def getPosition: Long = is.getPosition
 
-  def seek(pos: Long): Unit = is.seek(pos)
+  override def seek(pos: Long): Unit = is.seek(pos)
 }
 
 class WrappedPositionedDataOutputStream(os: PositionedOutputStream)
     extends DataOutputStream(os) with Positioned {
-  def getPosition: Long = os.getPosition
+  override def getPosition: Long = os.getPosition
 }
 
 class WrappedPositionOutputStream(os: OutputStream) extends OutputStream with Positioned {
@@ -44,7 +44,7 @@ class WrappedPositionOutputStream(os: OutputStream) extends OutputStream with Po
   override def close(): Unit =
     os.close()
 
-  def getPosition: Long = count
+  override def getPosition: Long = count
 }
 
 abstract class FSURL[URL <: FSURL[URL]] {
@@ -74,15 +74,15 @@ class BlobStorageFileStatus(
   size: Long,
 ) extends FileStatus {
   // NB: it is called getPath but it *must* return the URL *with* the scheme.
-  def getPath: String =
+  override def getPath: String =
     dropTrailingSlash(
       actualUrl
     ) // getPath is a backwards compatible method: in the past, Hail dropped trailing slashes
-  def getActualUrl: String = actualUrl
-  def getModificationTime: java.lang.Long = modificationTime
-  def getLen: Long = size
-  def isSymlink: Boolean = false
-  def getOwner: String = null
+  override def getActualUrl: String = actualUrl
+  override def getModificationTime: java.lang.Long = modificationTime
+  override def getLen: Long = size
+  override def isSymlink: Boolean = false
+  override def getOwner: String = null
 }
 
 class BlobStorageFileListEntry(
@@ -95,8 +95,8 @@ class BlobStorageFileListEntry(
       modificationTime,
       size,
     ) with FileListEntry {
-  def isDirectory: Boolean = isDir
-  def isFile: Boolean = !isDir
+  override def isDirectory: Boolean = isDir
+  override def isFile: Boolean = !isDir
   override def isFileOrFileAndDirectory = isFile
   override def toString: String = s"BSFLE($actualUrl $modificationTime $size $isDir)"
 
@@ -110,15 +110,16 @@ trait CompressionCodec {
 
 object GZipCompressionCodec extends CompressionCodec {
   // java.util.zip.GZIPInputStream does not support concatenated files/multiple blocks
-  def makeInputStream(is: InputStream): InputStream = new GzipCompressorInputStream(is, true)
+  override def makeInputStream(is: InputStream): InputStream =
+    new GzipCompressorInputStream(is, true)
 
-  def makeOutputStream(os: OutputStream): OutputStream = new GZIPOutputStream(os)
+  override def makeOutputStream(os: OutputStream): OutputStream = new GZIPOutputStream(os)
 }
 
 object BGZipCompressionCodec extends CompressionCodec {
-  def makeInputStream(is: InputStream): InputStream = new BGzipInputStream(is)
+  override def makeInputStream(is: InputStream): InputStream = new BGzipInputStream(is)
 
-  def makeOutputStream(os: OutputStream): OutputStream = new BGzipOutputStream(os)
+  override def makeOutputStream(os: OutputStream): OutputStream = new BGzipOutputStream(os)
 }
 
 class FileAndDirectoryException(message: String) extends RuntimeException(message)
@@ -203,7 +204,7 @@ abstract class FSSeekableInputStream extends InputStream with Seekable {
 
   protected def physicalSeek(newPos: Long): Unit
 
-  def seek(newPos: Long): Unit = {
+  override def seek(newPos: Long): Unit = {
     eof = false
     val distance = newPos - pos
     val bufferSeekPosition = bb.position() + distance
@@ -218,7 +219,7 @@ abstract class FSSeekableInputStream extends InputStream with Seekable {
     pos = newPos
   }
 
-  def getPosition: Long = pos
+  override def getPosition: Long = pos
 }
 
 abstract class FSPositionedOutputStream(val capacity: Int) extends OutputStream with Positioned {
@@ -226,9 +227,9 @@ abstract class FSPositionedOutputStream(val capacity: Int) extends OutputStream
   protected[this] val bb: ByteBuffer = ByteBuffer.allocate(capacity)
   protected[this] var pos: Long = 0
 
-  def flush(): Unit
+  override def flush(): Unit
 
-  def write(i: Int): Unit = {
+  override def write(i: Int): Unit = {
     if (bb.remaining() == 0)
       flush()
     bb.put(i.toByte)
@@ -249,7 +250,7 @@ abstract class FSPositionedOutputStream(val capacity: Int) extends OutputStream
     }
   }
 
-  def getPosition: Long = pos
+  override def getPosition: Long = pos
 }
 
 trait FS extends Serializable with Logging {
diff --git a/hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala b/hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala
index 4c5f33f251d..1c3cada149f 100644
--- a/hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala
+++ b/hail/hail/src/is/hail/io/fs/GoogleStorageFS.scala
@@ -1,6 +1,7 @@
 package is.hail.io.fs
 
 import is.hail.HailFeatureFlags
+import is.hail.collection.FastSeq
 import is.hail.io.fs.FSUtil.dropTrailingSlash
 import is.hail.io.fs.GoogleStorageFS.RequesterPaysFailure
 import is.hail.services.{isTransientError, retryTransientErrors}
@@ -144,10 +145,10 @@ class GoogleStorageFS(
   override def validUrl(filename: String): Boolean =
     filename.startsWith("gs://")
 
-  def getConfiguration(): Option[RequesterPaysConfig] =
+  override def getConfiguration(): Option[RequesterPaysConfig] =
     requesterPaysConfig
 
-  def setConfiguration(config: Any): Unit =
+  override def setConfiguration(config: Any): Unit =
     requesterPaysConfig = config.asInstanceOf[Option[RequesterPaysConfig]]
 
   private[this] def requesterPaysOptions[T](bucket: String, makeUserProjectOption: String => T)
@@ -186,7 +187,7 @@ class GoogleStorageFS(
       .getService
   }
 
-  def openNoCompression(url: URL): SeekableDataInputStream = retryTransientErrors {
+  override def openNoCompression(url: URL): SeekableDataInputStream = retryTransientErrors {
     val is: SeekableInputStream = new FSSeekableInputStream {
       private[this] var reader: ReadChannel = null
       private[this] var options: Option[Seq[BlobSourceOption]] = None
@@ -248,7 +249,7 @@ class GoogleStorageFS(
     new WrappedSeekableDataInputStream(is)
   }
 
-  def createNoCompression(url: URL): PositionedDataOutputStream = retryTransientErrors {
+  override def createNoCompression(url: URL): PositionedDataOutputStream = retryTransientErrors {
     logger.info(f"createNoCompression: $url")
 
     val blobId = BlobId.of(url.bucket, url.path)
@@ -376,7 +377,7 @@ class GoogleStorageFS(
     if (deleteSource) storage.delete(srcId): Unit
   }
 
-  def delete(url: URL, recursive: Boolean): Unit =
+  override def delete(url: URL, recursive: Boolean): Unit =
     retryTransientErrors[Unit] {
       if (recursive) {
         var page = retryTransientErrors {
@@ -418,7 +419,7 @@ class GoogleStorageFS(
       }
     }
 
-  def glob(url: URL): Array[FileListEntry] = retryTransientErrors {
+  override def glob(url: URL): Array[FileListEntry] = retryTransientErrors {
     globWithPrefix(url.withPath(""), path = dropTrailingSlash(url.path))
   }
 
@@ -500,7 +501,7 @@ class GoogleStorageFS(
       url.bucket,
     )
 
-  def makeQualified(filename: String): String = {
+  override def makeQualified(filename: String): String = {
     if (!filename.startsWith("gs://"))
       throw new IllegalArgumentException(s"Invalid path, expected gs://bucket/path $filename")
     filename
diff --git a/hail/hail/src/is/hail/io/fs/HadoopFS.scala b/hail/hail/src/is/hail/io/fs/HadoopFS.scala
index 0241f4840f7..e8532341652 100644
--- a/hail/hail/src/is/hail/io/fs/HadoopFS.scala
+++ b/hail/hail/src/is/hail/io/fs/HadoopFS.scala
@@ -13,21 +13,21 @@ import org.apache.hadoop.fs.{EtagSource, FSDataInputStream, FSDataOutputStream,
 class HadoopFileListEntry(fs: hadoop.fs.FileStatus) extends FileListEntry {
   val normalizedPath = fs.getPath
 
-  def getPath: String = fs.getPath.toString
+  override def getPath: String = fs.getPath.toString
 
-  def getActualUrl: String = fs.getPath.toString
+  override def getActualUrl: String = fs.getPath.toString
 
-  def getModificationTime: java.lang.Long = fs.getModificationTime
+  override def getModificationTime: java.lang.Long = fs.getModificationTime
 
-  def getLen: Long = fs.getLen
+  override def getLen: Long = fs.getLen
 
-  def isDirectory: Boolean = fs.isDirectory
+  override def isDirectory: Boolean = fs.isDirectory
 
-  def isFile: Boolean = fs.isFile
+  override def isFile: Boolean = fs.isFile
 
-  def isSymlink: Boolean = fs.isSymlink
+  override def isSymlink: Boolean = fs.isSymlink
 
-  def getOwner: String = fs.getOwner
+  override def getOwner: String = fs.getOwner
 }
 
 object HadoopFS {
@@ -47,7 +47,7 @@ object HadoopFS {
           closed = true
         }
 
-      def getPosition: Long = os.getPos
+      override def getPosition: Long = os.getPos
     }
 
   def toSeekableInputStream(is: FSDataInputStream): SeekableInputStream =
@@ -66,9 +66,9 @@ object HadoopFS {
           closed = true
         }
 
-      def seek(pos: Long): Unit = is.seek(pos)
+      override def seek(pos: Long): Unit = is.seek(pos)
 
-      def getPosition: Long = is.getPos
+      override def getPosition: Long = is.getPos
     }
 }
 
@@ -93,19 +93,19 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
   override def validUrl(filename: String): Boolean =
     Try(getFileSystem(filename)).isSuccess
 
-  def getConfiguration(): SerializableHadoopConfiguration = conf
+  override def getConfiguration(): SerializableHadoopConfiguration = conf
 
-  def setConfiguration(_conf: Any): Unit =
+  override def setConfiguration(_conf: Any): Unit =
     conf = _conf.asInstanceOf[SerializableHadoopConfiguration]
 
-  def createNoCompression(url: URL): PositionedDataOutputStream = {
+  override def createNoCompression(url: URL): PositionedDataOutputStream = {
     val os = url.hadoopFs.create(url.hadoopPath)
     new WrappedPositionedDataOutputStream(
       HadoopFS.toPositionedOutputStream(os)
     )
   }
 
-  def openNoCompression(url: URL): SeekableDataInputStream = {
+  override def openNoCompression(url: URL): SeekableDataInputStream = {
     val is =
       try
         url.hadoopFs.open(url.hadoopPath)
@@ -126,7 +126,7 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
   def getFileSystem(filename: String): hadoop.fs.FileSystem =
     new hadoop.fs.Path(filename).getFileSystem(conf.value)
 
-  def listDirectory(url: URL): Array[FileListEntry] = {
+  override def listDirectory(url: URL): Array[FileListEntry] = {
     val statuses = url.hadoopFs.globStatus(url.hadoopPath)
     if (statuses == null) {
       throw new FileNotFoundException(url.toString)
@@ -147,7 +147,7 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
   def rmtree(dirname: String): Unit =
     getFileSystem(dirname).delete(new hadoop.fs.Path(dirname), true)
 
-  def delete(url: URL, recursive: Boolean): Unit =
+  override def delete(url: URL, recursive: Boolean): Unit =
     url.hadoopFs.delete(url.hadoopPath, recursive): Unit
 
   override def globAll(filenames: Iterable[String]): Array[FileListEntry] = {
@@ -159,7 +159,7 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
     }.toArray
   }
 
-  def glob(url: URL): Array[FileListEntry] = {
+  override def glob(url: URL): Array[FileListEntry] = {
     var files = url.hadoopFs.globStatus(url.hadoopPath)
     if (files == null)
       files = Array.empty
@@ -177,7 +177,7 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
     fle
   }
 
-  def fileListEntry(url: URL): FileListEntry =
+  override def fileListEntry(url: URL): FileListEntry =
     new HadoopFileListEntry(url.hadoopFs.getFileStatus(url.hadoopPath))
 
   override def eTag(url: URL): Option[String] =
@@ -186,7 +186,7 @@ class HadoopFS(private[this] var conf: SerializableHadoopConfiguration) extends
     else
       None
 
-  def makeQualified(path: String): String = {
+  override def makeQualified(path: String): String = {
     val ppath = new hadoop.fs.Path(path)
     val pathFS = ppath.getFileSystem(conf.value)
     pathFS.makeQualified(ppath).toString
diff --git a/hail/hail/src/is/hail/io/fs/RouterFS.scala b/hail/hail/src/is/hail/io/fs/RouterFS.scala
index 39104f43769..daf83137c10 100644
--- a/hail/hail/src/is/hail/io/fs/RouterFS.scala
+++ b/hail/hail/src/is/hail/io/fs/RouterFS.scala
@@ -1,8 +1,9 @@
 package is.hail.io.fs
 
 import is.hail.HailFeatureFlags
+import is.hail.collection.FastSeq
 import is.hail.services.oauth2.{AzureCloudCredentials, GoogleCloudCredentials}
-import is.hail.utils.{FastSeq, SerializableHadoopConfiguration}
+import is.hail.utils.SerializableHadoopConfiguration
 
 import java.io.Serializable
 import java.nio.file.Path
@@ -91,28 +92,28 @@ class RouterFS(fss: IndexedSeq[FS]) extends FS {
   override def createNoCompression(url: RouterFSURL): PositionedDataOutputStream =
     url.fs.createNoCompression(url.url)
 
-  def openNoCompression(url: URL): SeekableDataInputStream =
+  override def openNoCompression(url: URL): SeekableDataInputStream =
     url.fs.openNoCompression(url.url)
 
   override def mkDir(url: URL): Unit = url.fs.mkDir(url.url)
 
-  def delete(url: URL, recursive: Boolean) = url.fs.delete(url.url, recursive)
+  override def delete(url: URL, recursive: Boolean) = url.fs.delete(url.url, recursive)
 
-  def listDirectory(url: URL): Array[FileListEntry] = url.fs.listDirectory(url.url)
+  override def listDirectory(url: URL): Array[FileListEntry] = url.fs.listDirectory(url.url)
 
-  def glob(url: URL): Array[FileListEntry] = url.fs.glob(url.url)
+  override def glob(url: URL): Array[FileListEntry] = url.fs.glob(url.url)
 
-  def fileStatus(url: URL): FileStatus = url.fs.fileStatus(url.url)
+  override def fileStatus(url: URL): FileStatus = url.fs.fileStatus(url.url)
 
-  def fileListEntry(url: URL): FileListEntry = url.fs.fileListEntry(url.url)
+  override def fileListEntry(url: URL): FileListEntry = url.fs.fileListEntry(url.url)
 
   override def eTag(url: URL): Option[String] = url.fs.eTag(url.url)
 
-  def makeQualified(path: String): String = lookupFS(path).makeQualified(path)
+  override def makeQualified(path: String): String = lookupFS(path).makeQualified(path)
 
-  def getConfiguration(): Any = fss.map(_.getConfiguration())
+  override def getConfiguration(): Any = fss.map(_.getConfiguration())
 
-  def setConfiguration(config: Any): Unit =
+  override def setConfiguration(config: Any): Unit =
     fss.zip(config.asInstanceOf[IndexedSeq[_]]).foreach { case (fs: FS, config: Any) =>
       fs.setConfiguration(config)
     }
diff --git a/hail/hail/src/is/hail/io/fs/package.scala b/hail/hail/src/is/hail/io/fs/package.scala
index 39aaa8a54d4..b08f014bbbb 100644
--- a/hail/hail/src/is/hail/io/fs/package.scala
+++ b/hail/hail/src/is/hail/io/fs/package.scala
@@ -2,6 +2,8 @@ package is.hail.io
 
 import java.io.{DataInputStream, DataOutputStream, InputStream, OutputStream}
 
+import org.apache.hadoop.fs.PathIOException
+
 package object fs {
   type PositionedInputStream = InputStream with Positioned
 
@@ -19,4 +21,27 @@ package object fs {
         os
       )
     )
+
+  private[this] val PartRegex = """.*/?part-(\d+).*""".r
+
+  def getPartNumber(fname: String): Int =
+    fname match {
+      case PartRegex(i) => i.toInt
+      case _ => throw new PathIOException(s"invalid partition file '$fname'")
+    }
+
+  private[this] val Kilo: Long = 1024
+  private[this] val Mega: Long = Kilo * 1024
+  private[this] val Giga: Long = Mega * 1024
+  private[this] val Tera: Long = Giga * 1024
+
+  def readableBytes(bytes: Long): String =
+    if (bytes < Kilo) bytes.toString
+    else if (bytes < Mega) formatDigits(bytes, Kilo) + "K"
+    else if (bytes < Giga) formatDigits(bytes, Mega) + "M"
+    else if (bytes < Tera) formatDigits(bytes, Giga) + "G"
+    else formatDigits(bytes, Tera) + "T"
+
+  private def formatDigits(n: Long, factor: Long): String =
+    "%.1f".format(n / factor.toDouble)
 }
diff --git a/hail/hail/src/is/hail/io/gen/ExportBGEN.scala b/hail/hail/src/is/hail/io/gen/ExportBGEN.scala
index bd478bf873c..f4af1cf6594 100644
--- a/hail/hail/src/is/hail/io/gen/ExportBGEN.scala
+++ b/hail/hail/src/is/hail/io/gen/ExportBGEN.scala
@@ -1,6 +1,6 @@
 package is.hail.io.gen
 
-import is.hail.expr.ir.ByteArrayBuilder
+import is.hail.collection.ByteArrayBuilder
 import is.hail.io.fs.FS
 
 object BgenWriter {
diff --git a/hail/hail/src/is/hail/io/gen/ExportGen.scala b/hail/hail/src/is/hail/io/gen/ExportGen.scala
index bd62fffe52e..cd56f750350 100644
--- a/hail/hail/src/is/hail/io/gen/ExportGen.scala
+++ b/hail/hail/src/is/hail/io/gen/ExportGen.scala
@@ -60,7 +60,7 @@ class GenAnnotationView(rowType: PStruct) extends View {
   private var cachedVarid: String = _
   private var cachedRsid: String = _
 
-  def set(offset: Long): Unit = {
+  override def set(offset: Long): Unit = {
     assert(rowType.isFieldDefined(offset, varidIdx))
     assert(rowType.isFieldDefined(offset, rsidIdx))
     this.rsidOffset = rowType.loadField(offset, rsidIdx)
diff --git a/hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala b/hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala
index a24e4f6d283..7016b73cf9f 100644
--- a/hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala
+++ b/hail/hail/src/is/hail/io/hadoop/ByteArrayOutputFormat.scala
@@ -12,11 +12,11 @@ class ByteArrayOutputFormat extends FileOutputFormat[NullWritable, BytesOnlyWrit
   class ByteArrayRecordWriter(out: DataOutputStream)
       extends RecordWriter[NullWritable, BytesOnlyWritable] {
 
-    def write(key: NullWritable, value: BytesOnlyWritable): Unit =
+    override def write(key: NullWritable, value: BytesOnlyWritable): Unit =
       if (value != null)
         value.write(out)
 
-    def close(reporter: Reporter): Unit =
+    override def close(reporter: Reporter): Unit =
       out.close()
   }
 
diff --git a/hail/hail/src/is/hail/io/index/IndexReader.scala b/hail/hail/src/is/hail/io/index/IndexReader.scala
index 593171afba2..ad7dfc3a9e1 100644
--- a/hail/hail/src/is/hail/io/index/IndexReader.scala
+++ b/hail/hail/src/is/hail/io/index/IndexReader.scala
@@ -3,20 +3,21 @@ package is.hail.io.index
 import is.hail.annotations._
 import is.hail.asm4s.HailClassLoader
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIndexedSeq
 import is.hail.io._
 import is.hail.io.fs.FS
 import is.hail.rvd.{AbstractIndexSpec, PartitionBoundOrdering}
 import is.hail.types.physical.PStruct
 import is.hail.types.virtual.{TStruct, Type, TypeSerializer}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import java.io.InputStream
 import java.util
 import java.util.Map.Entry
 
 import org.apache.spark.sql.Row
-import org.json4s.Formats
+import org.json4s.{DefaultFormats, Formats}
 import org.json4s.jackson.JsonMethods
 
 object IndexReaderBuilder {
@@ -53,7 +54,7 @@ object IndexReader {
       JsonMethods.parse(in)
         .removeField { case (f, _) => f == "keyType" || f == "annotationType" }
     }
-    implicit val formats: Formats = defaultJSONFormats
+    implicit val formats: Formats = DefaultFormats
     jv.extract[IndexMetadataUntypedJSON]
   }
 
@@ -64,7 +65,7 @@ object IndexReader {
 
   def readTypes(fs: FS, path: String): (Type, Type) = {
     val jv = using(fs.open(path + "/metadata.json.gz"))(in => JsonMethods.parse(in))
-    implicit val formats: Formats = defaultJSONFormats + new TypeSerializer
+    implicit val formats: Formats = DefaultFormats + new TypeSerializer
     val metadata = jv.extract[IndexMetadata]
     metadata.keyType -> metadata.annotationType
   }
@@ -250,7 +251,7 @@ class IndexReader(
     var localPos = 0
     var leafNode: LeafNode = _
 
-    def next(): LeafChild = {
+    override def next(): LeafChild = {
       assert(hasNext)
 
       if (leafNode == null || localPos >= leafNode.children.length) {
@@ -265,7 +266,7 @@ class IndexReader(
       child
     }
 
-    def hasNext: Boolean = pos < end
+    override def hasNext: Boolean = pos < end
 
     def seek(key: Annotation): Unit = {
       val newPos = lowerBound(key)
@@ -281,7 +282,7 @@ class IndexReader(
   def iterateUntil(key: Annotation): Iterator[LeafChild] =
     iterator(0, lowerBound(key))
 
-  def close(): Unit = {
+  override def close(): Unit = {
     leafDecoder.close()
     internalDecoder.close()
     logger.info(s"Index reader cache queries: ${cacheHits + cacheMisses}")
diff --git a/hail/hail/src/is/hail/io/index/IndexWriter.scala b/hail/hail/src/is/hail/io/index/IndexWriter.scala
index 3cb5a37d78a..8b30ab0207b 100644
--- a/hail/hail/src/is/hail/io/index/IndexWriter.scala
+++ b/hail/hail/src/is/hail/io/index/IndexWriter.scala
@@ -1,11 +1,13 @@
 package is.hail.io.index
 
 import is.hail.annotations.{Annotation, Region, RegionPool}
-import is.hail.asm4s.{HailClassLoader, _}
+import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeOutputBuffer
 import is.hail.backend.{ExecuteContext, HailStateManager, HailTaskContext}
+import is.hail.collection.{FastSeq, IntArrayBuilder, LongArrayBuilder}
 import is.hail.expr.ir.{
   CodeParam, EmitClassBuilder, EmitCodeBuilder, EmitFunctionBuilder, EmitMethodBuilder, IEmitCode,
-  IntArrayBuilder, LongArrayBuilder, ParamType,
+  ParamType,
 }
 import is.hail.io._
 import is.hail.io.fs.FS
@@ -17,7 +19,7 @@ import is.hail.types.physical.stypes.concrete.{SBaseStructPointer, SBaseStructPo
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
 import is.hail.types.virtual.Type
 import is.hail.utils._
-import is.hail.utils.richUtils.ByteTrackingOutputStream
+import is.hail.utils.implicits.ByteTrackingOutputStream
 
 import scala.collection.mutable.ArrayBuffer
 
@@ -121,7 +123,7 @@ class IndexWriter(
 
   def trackedOS(): ByteTrackingOutputStream = comp.trackedOS()
 
-  def close(): Unit = {
+  override def close(): Unit = {
     region.close()
     comp.close()
   }
diff --git a/hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala b/hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala
index aa0430e7d14..b91f4e538f8 100644
--- a/hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala
+++ b/hail/hail/src/is/hail/io/index/LeafNodeBuilder.scala
@@ -2,6 +2,7 @@ package is.hail.io.index
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, SettableBuilder, Value}
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.io.OutputBuffer
 import is.hail.types.encoded.EType
@@ -10,7 +11,6 @@ import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{SBaseStructPointer, SBaseStructPointerSettable}
 import is.hail.types.physical.stypes.interfaces.{primitive, SBaseStructValue}
 import is.hail.types.virtual.{TStruct, Type}
-import is.hail.utils._
 
 object LeafNodeBuilder {
   def virtualType(keyType: Type, annotationType: Type): TStruct =
diff --git a/hail/hail/src/is/hail/io/index/StagedIndexReader.scala b/hail/hail/src/is/hail/io/index/StagedIndexReader.scala
index 018342e025d..b8314e21f70 100644
--- a/hail/hail/src/is/hail/io/index/StagedIndexReader.scala
+++ b/hail/hail/src/is/hail/io/index/StagedIndexReader.scala
@@ -2,7 +2,9 @@ package is.hail.io.index
 
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeInputBuffer
 import is.hail.backend.TaskFinalizer
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
   BinarySearch, EmitCode, EmitCodeBuilder, EmitMethodBuilder, EmitValue, IEmitCode,
 }
diff --git a/hail/hail/src/is/hail/io/package.scala b/hail/hail/src/is/hail/io/package.scala
index 51724ed5dff..75f75273bc4 100644
--- a/hail/hail/src/is/hail/io/package.scala
+++ b/hail/hail/src/is/hail/io/package.scala
@@ -1,19 +1,17 @@
 package is.hail
 
-import is.hail.io.fs.FS
+import is.hail.collection.implicits.toRichIterable
+import is.hail.io.fs.{readableBytes, FS, FileListEntry}
 import is.hail.types.virtual.Type
 import is.hail.utils._
 
 import java.io.OutputStreamWriter
-import java.nio.charset._
 
-package object io {
+package object io extends Logging {
   type VCFFieldAttributes = Map[String, String]
   type VCFAttributes = Map[String, VCFFieldAttributes]
   type VCFMetadata = Map[String, VCFAttributes]
 
-  val utfCharset = Charset.forName("UTF-8")
-
   def exportTypes(filename: String, fs: FS, info: Array[(String, Type)]): Unit = {
     val sb = new StringBuilder
     using(new OutputStreamWriter(fs.create(filename))) { out =>
@@ -26,4 +24,49 @@ package object io {
       out.write(sb.result())
     }
   }
+
+  def checkGzipOfGlobbedFiles(
+    globPaths: Seq[String],
+    fileListEntries: Array[FileListEntry],
+    forceGZ: Boolean,
+    gzAsBGZ: Boolean,
+    maxSizeMB: Int = 128,
+  ): Unit = {
+    if (fileListEntries.isEmpty)
+      fatal(s"arguments refer to no files: ${globPaths.toIndexedSeq}.")
+
+    if (!gzAsBGZ) {
+      fileListEntries.foreach { fileListEntry =>
+        val path = fileListEntry.getPath
+        if (path.endsWith(".gz"))
+          checkGzippedFile(fileListEntry, forceGZ, false, maxSizeMB)
+      }
+    }
+  }
+
+  def checkGzippedFile(
+    fileListEntry: FileListEntry,
+    forceGZ: Boolean,
+    gzAsBGZ: Boolean,
+    maxSizeMB: Int = 128,
+  ): Unit =
+    if (!forceGZ && !gzAsBGZ)
+      fatal(
+        s"""Cannot load file '${fileListEntry.getPath}'
+           |  .gz cannot be loaded in parallel. Is the file actually *block* gzipped?
+           |  If the file is actually block gzipped (even though its extension is .gz),
+           |  use the 'force_bgz' argument to treat all .gz file extensions as .bgz.
+           |  If you are sure that you want to load a non-block-gzipped file serially
+           |  on one core, use the 'force' argument.""".stripMargin
+      )
+    else if (!gzAsBGZ) {
+      val fileSize = fileListEntry.getLen
+      if (fileSize > 1024 * 1024 * maxSizeMB)
+        logger.warn(
+          s"""file '${fileListEntry.getPath}' is ${readableBytes(fileSize)}
+             |  It will be loaded serially (on one core) due to usage of the 'force' argument.
+             |  If it is actually block-gzipped, either rename to .bgz or use the 'force_bgz'
+             |  argument.""".stripMargin
+        )
+    }
 }
diff --git a/hail/hail/src/is/hail/io/plink/LoadPlink.scala b/hail/hail/src/is/hail/io/plink/LoadPlink.scala
index afed2c87f12..98fcaed3a22 100644
--- a/hail/hail/src/is/hail/io/plink/LoadPlink.scala
+++ b/hail/hail/src/is/hail/io/plink/LoadPlink.scala
@@ -3,6 +3,9 @@ package is.hail.io.plink
 import is.hail.annotations.{Region, RegionValueBuilder}
 import is.hail.asm4s.HailClassLoader
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat._
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs.Literal
@@ -15,8 +18,7 @@ import is.hail.types.physical._
 import is.hail.types.virtual._
 import is.hail.utils._
 import is.hail.utils.StringEscapeUtils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.utils.implicits.{toRichContextIterator, toRichInputStream}
 import is.hail.variant._
 
 import java.io.{ObjectInputStream, ObjectOutputStream}
@@ -74,9 +76,8 @@ object LoadPlink extends Logging {
         n += 1
       }
     }
-    val variants = vs.result().sortInPlaceBy(_.locusAlleles)(
-      locusAllelesType.ordering(ctx.stateManager).toOrdering
-    ).array
+    implicit val ord = locusAllelesType.ordering(ctx.stateManager).toOrdering
+    val variants = vs.result().sortInPlaceBy(_.locusAlleles).array
     (n, variants)
   }
 
@@ -367,16 +368,16 @@ class MatrixPLINKReader(
   partitioner: RVDPartitioner,
 ) extends MatrixHybridReader {
 
-  def rowUIDType = TInt64
-  def colUIDType = TInt64
+  override def rowUIDType = TInt64
+  override def colUIDType = TInt64
 
-  def pathsUsed: Seq[String] = FastSeq(params.bed, params.bim, params.fam)
+  override def pathsUsed: Seq[String] = FastSeq(params.bed, params.bim, params.fam)
 
   def nSamples: Int = sampleInfo.length
 
   val columnCount: Option[Int] = Some(nSamples)
 
-  def partitionCounts: Option[IndexedSeq[Long]] = None
+  override def partitionCounts: Option[IndexedSeq[Long]] = None
 
   val globals = Row(sampleInfo.zipWithIndex.map { case (s, idx) =>
     Row((0 until s.length).map(s.apply) :+ idx.toLong: _*)
@@ -492,7 +493,7 @@ class MatrixPLINKReader(
               offset = newOffset
             }
 
-            is.readFully(input, 0, input.length)
+            is.readFully(input)
 
             rvb.start(requestedPType)
             rvb.startStruct()
@@ -582,7 +583,7 @@ class MatrixPLINKReader(
     decomposeWithName(params, "MatrixPLINKReader")
   }
 
-  def renderShort(): String = defaultRender()
+  override def renderShort(): String = defaultRender()
 
   override def hashCode(): Int = params.hashCode()
 
diff --git a/hail/hail/src/is/hail/io/reference/IndexedFastaSequenceFile.scala b/hail/hail/src/is/hail/io/reference/IndexedFastaSequenceFile.scala
index 72ba195b78a..697f04bf904 100644
--- a/hail/hail/src/is/hail/io/reference/IndexedFastaSequenceFile.scala
+++ b/hail/hail/src/is/hail/io/reference/IndexedFastaSequenceFile.scala
@@ -1,7 +1,8 @@
 package is.hail.io.reference
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.io.fs.FS
-import is.hail.utils.{fatal, toRichIterable}
+import is.hail.utils.fatal
 import is.hail.variant.ReferenceGenome
 
 object IndexedFastaSequenceFile {
diff --git a/hail/hail/src/is/hail/io/tabix/TabixReader.scala b/hail/hail/src/is/hail/io/tabix/TabixReader.scala
index 891e90616b6..57a07851515 100644
--- a/hail/hail/src/is/hail/io/tabix/TabixReader.scala
+++ b/hail/hail/src/is/hail/io/tabix/TabixReader.scala
@@ -1,10 +1,11 @@
 package is.hail.io.tabix
 
-import is.hail.expr.ir.IntArrayBuilder
+import is.hail.collection.IntArrayBuilder
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.io.compress.BGzipLineReader
 import is.hail.io.fs.FS
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.utils.implicits.toRichInputStream
 
 import scala.collection.mutable
 
@@ -26,8 +27,7 @@ class Tabix(
 )
 
 case class TbiPair(var _1: Long, var _2: Long) extends java.lang.Comparable[TbiPair] {
-  @Override
-  def compareTo(other: TbiPair): Int = TbiOrd.compare(this, other)
+  override def compareTo(other: TbiPair): Int = TbiOrd.compare(this, other)
 }
 
 object TbiPair {
@@ -35,7 +35,7 @@ object TbiPair {
 }
 
 object TbiOrd extends Ordering[TbiPair] {
-  def compare(u: TbiPair, v: TbiPair): Int = if (u._1 == v._1) {
+  override def compare(u: TbiPair, v: TbiPair): Int = if (u._1 == v._1) {
     0
   } else if (less64(u._1, v._1)) {
     -1
diff --git a/hail/hail/src/is/hail/io/vcf/ExportVCF.scala b/hail/hail/src/is/hail/io/vcf/ExportVCF.scala
index 3c7463401e0..353f877974a 100644
--- a/hail/hail/src/is/hail/io/vcf/ExportVCF.scala
+++ b/hail/hail/src/is/hail/io/vcf/ExportVCF.scala
@@ -1,5 +1,6 @@
 package is.hail.io.vcf
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.io.{VCFAttributes, VCFFieldAttributes, VCFMetadata}
 import is.hail.io.compress.{BGzipLineReader, BGzipOutputStream}
 import is.hail.io.fs.FS
@@ -149,7 +150,7 @@ object ExportVCF extends Logging {
     val sb = new StringBuilder()
 
     sb.append("##fileformat=VCFv4.2\n")
-    sb.append(s"##hailversion=${hail.HAIL_PRETTY_VERSION}\n")
+    sb.append(s"##hailversion=${hail.PrettyVersion}\n")
 
     entryType.fields.foreach { f =>
       val attrs = getAttributes("format", f.name, metadata).getOrElse(Map.empty[String, String])
diff --git a/hail/hail/src/is/hail/io/vcf/LoadVCF.scala b/hail/hail/src/is/hail/io/vcf/LoadVCF.scala
index 285fabb75b1..168a2123315 100644
--- a/hail/hail/src/is/hail/io/vcf/LoadVCF.scala
+++ b/hail/hail/src/is/hail/io/vcf/LoadVCF.scala
@@ -4,6 +4,8 @@ import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.{BroadcastValue, ExecuteContext, HailStateManager}
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.{FastSeq, MissingArrayBuilder}
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir.{
   CloseableIterator, EmitCode, EmitCodeBuilder, EmitMethodBuilder, GenericLine, GenericLines,
@@ -12,7 +14,7 @@ import is.hail.expr.ir.{
 import is.hail.expr.ir.defs.{Literal, PartitionReader}
 import is.hail.expr.ir.lowering.TableStage
 import is.hail.expr.ir.streams.StreamProducer
-import is.hail.io.{VCFAttributes, VCFMetadata}
+import is.hail.io.{checkGzipOfGlobbedFiles, VCFAttributes, VCFMetadata}
 import is.hail.io.fs.{FS, FileListEntry}
 import is.hail.io.tabix._
 import is.hail.io.vcf.LoadVCF.{getHeaderLines, parseHeader}
@@ -23,6 +25,7 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.interfaces.{SBaseStructValue, SStreamValue}
 import is.hail.types.virtual._
 import is.hail.utils._
+import is.hail.utils.implicits.toTruncatable
 import is.hail.variant._
 
 import scala.annotation.meta.param
@@ -1522,7 +1525,7 @@ object LoadVCF extends Logging {
         val abf = new MissingArrayBuilder[Float]
         val abd = new MissingArrayBuilder[Double]
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           while (!present && it.hasNext) {
             val lwc = it.next()
             val line = lwc.value
@@ -1583,7 +1586,7 @@ object LoadVCF extends Logging {
           present
         }
 
-        def next(): Long = {
+        override def next(): Long = {
           // call hasNext to advance if necessary
           if (!hasNext)
             throw new java.util.NoSuchElementException()
@@ -1688,9 +1691,9 @@ class PartitionedVCFRDD(
   val contigRemappingBc =
     if (reverseContigMapping.size != 0) sparkContext.broadcast(reverseContigMapping) else null
 
-  protected def getPartitions: Array[Partition] = _partitions
+  override protected def getPartitions: Array[Partition] = _partitions
 
-  def compute(split: Partition, context: TaskContext): Iterator[WithContext[String]] = {
+  override def compute(split: Partition, context: TaskContext): Iterator[WithContext[String]] = {
     val p = split.asInstanceOf[PartitionedVCFPartition]
 
     val chromToQuery = if (contigRemappingBc != null)
@@ -1715,9 +1718,9 @@ class PartitionedVCFRDD(
       private var l = lines.next()
       private var curIdx: Long = lines.getCurIdx()
 
-      def hasNext: Boolean = l != null
+      override def hasNext: Boolean = l != null
 
-      def next(): WithContext[String] = {
+      override def next(): WithContext[String] = {
         assert(l != null)
         val n = l
         l = lines.next()
@@ -1917,8 +1920,8 @@ class MatrixVCFReader(
 
   LoadVCF.warnDuplicates(sampleIDs)
 
-  def rowUIDType = TTuple(TInt64, TInt64)
-  def colUIDType = TInt64
+  override def rowUIDType = TTuple(TInt64, TInt64)
+  override def colUIDType = TInt64
 
   val (infoPType, rowValuePType, formatPType) = header.getPTypes(
     params.arrayElementsRequired,
@@ -1926,7 +1929,7 @@ class MatrixVCFReader(
     params.callFields,
   )
 
-  def fullMatrixTypeWithoutUIDs: MatrixType = MatrixType(
+  override def fullMatrixTypeWithoutUIDs: MatrixType = MatrixType(
     globalType = TStruct.empty,
     colType = TStruct("s" -> TString),
     colKey = Array("s"),
@@ -1958,13 +1961,13 @@ class MatrixVCFReader(
     fullType.key,
   )
 
-  def pathsUsed: Seq[String] = params.files
+  override def pathsUsed: Seq[String] = params.files
 
   def nCols: Int = sampleIDs.length
 
   val columnCount: Option[Int] = Some(nCols)
 
-  def partitionCounts: Option[IndexedSeq[Long]] = None
+  override def partitionCounts: Option[IndexedSeq[Long]] = None
 
   def partitioner(sm: HailStateManager): Option[RVDPartitioner] =
     params.partitionsJSON.map { partitionsJSON =>
@@ -2140,7 +2143,7 @@ class MatrixVCFReader(
     decomposeWithName(params, "MatrixVCFReader")
   }
 
-  def renderShort(): String = defaultRender()
+  override def renderShort(): String = defaultRender()
 
   override def hashCode(): Int = params.hashCode()
 
@@ -2189,7 +2192,7 @@ case class GVCFPartitionReader(
 
   lazy val fullRowType: TStruct = fullRowPType.virtualType
 
-  def rowRequiredness(requestedType: TStruct): RStruct =
+  override def rowRequiredness(requestedType: TStruct): RStruct =
     VirtualTypeWithReq(tcoerce[PStruct](fullRowPType.subsetTo(requestedType))).r.asInstanceOf[
       RStruct
     ]
@@ -2199,7 +2202,7 @@ case class GVCFPartitionReader(
     decomposeWithName(this, "MatrixVCFReader")
   }
 
-  def emitStream(
+  override def emitStream(
     ctx: ExecuteContext,
     cb: EmitCodeBuilder,
     mb: EmitMethodBuilder[_],
diff --git a/hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala b/hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala
index ad5cf64e400..37164d1df7b 100644
--- a/hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala
+++ b/hail/hail/src/is/hail/io/vcf/TabixReadVCFIterator.scala
@@ -2,11 +2,12 @@ package is.hail.io.vcf
 
 import is.hail.annotations.{Region, RegionValueBuilder}
 import is.hail.backend.HailStateManager
+import is.hail.collection.MissingArrayBuilder
 import is.hail.expr.ir.{CloseableIterator, GenericLine}
 import is.hail.io.fs.FS
 import is.hail.io.tabix.{TabixLineIterator, TabixReader}
 import is.hail.types.physical.PStruct
-import is.hail.utils.{fatal, makeJavaSet, MissingArrayBuilder, TextInputFilterAndReplace}
+import is.hail.utils.{fatal, makeJavaSet, TextInputFilterAndReplace}
 import is.hail.variant.ReferenceGenome
 
 class TabixReadVCFIterator(
@@ -48,9 +49,9 @@ class TabixReadVCFIterator(
       private[this] var l = lines.next()
       private[this] var curIdx: Long = lines.getCurIdx()
       private[this] val inner = new Iterator[GenericLine] {
-        def hasNext: Boolean = l != null
+        override def hasNext: Boolean = l != null
 
-        def next(): GenericLine = {
+        override def next(): GenericLine = {
           assert(l != null)
           try {
             val n = l
@@ -85,11 +86,11 @@ class TabixReadVCFIterator(
         start <= pos && pos <= end
       }
 
-      def hasNext: Boolean = inner.hasNext
+      override def hasNext: Boolean = inner.hasNext
 
-      def next(): GenericLine = inner.next()
+      override def next(): GenericLine = inner.next()
 
-      def close(): Unit = lines.close()
+      override def close(): Unit = lines.close()
     }
   }
 
diff --git a/hail/hail/src/is/hail/linalg/BLAS.scala b/hail/hail/src/is/hail/linalg/BLAS.scala
index bee4988b60f..a9776f0d2fd 100644
--- a/hail/hail/src/is/hail/linalg/BLAS.scala
+++ b/hail/hail/src/is/hail/linalg/BLAS.scala
@@ -11,7 +11,7 @@ import com.sun.jna.ptr.{DoubleByReference, FloatByReference, IntByReference}
 
 object BLAS extends Logging {
   private[this] val libraryInstance = ThreadLocal.withInitial(new Supplier[BLASLibrary]() {
-    def get() = {
+    override def get() = {
       val standard = Native.load("blas", classOf[BLASLibrary]).asInstanceOf[BLASLibrary]
 
       verificationTest(standard) match {
diff --git a/hail/hail/src/is/hail/linalg/BlockMatrix.scala b/hail/hail/src/is/hail/linalg/BlockMatrix.scala
index 512672608a0..95b41d9ed7f 100644
--- a/hail/hail/src/is/hail/linalg/BlockMatrix.scala
+++ b/hail/hail/src/is/hail/linalg/BlockMatrix.scala
@@ -3,20 +3,21 @@ package is.hail.linalg
 import is.hail.annotations._
 import is.hail.backend.{BroadcastValue, ExecuteContext, HailStateManager}
 import is.hail.backend.spark.{SparkBackend, SparkTaskContext}
-import is.hail.expr.ir.{IntArrayBuilder, TableReader, TableValue, ThreefryRandomEngine}
+import is.hail.collection.{FastSeq, IntArrayBuilder}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
+import is.hail.expr.ir.{partFile, TableReader, TableValue, ThreefryRandomEngine}
 import is.hail.io._
 import is.hail.io.fs.FS
 import is.hail.io.index.IndexWriter
+import is.hail.linalg.implicits._
 import is.hail.rvd.{RVD, RVDContext}
 import is.hail.sparkextras.{ContextRDD, OriginUnionPartition, OriginUnionRDD}
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical._
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.richUtils.{
-  ByteTrackingOutputStream, RichArray, RichContextRDD, RichDenseMatrixDouble,
-}
+import is.hail.utils.implicits.ByteTrackingOutputStream
 
 import scala.collection.immutable.NumericRange
 
@@ -48,7 +49,7 @@ class CollectMatricesRDD(@transient var bms: IndexedSeq[BlockMatrix])
   private val nBlocks = bms.map(_.blocks.getNumPartitions)
   private val firstPartition = nBlocks.scan(0)(_ + _).init
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     bms.iterator.zipWithIndex.map { case (bm, i) =>
       CollectMatricesRDDPartition(
         i,
@@ -65,7 +66,7 @@ class CollectMatricesRDD(@transient var bms: IndexedSeq[BlockMatrix])
     bms.zipWithIndex.map { case (bm, i) =>
       val n = nBlocks(i)
       new NarrowDependency(bm.blocks) {
-        def getParents(j: Int): Seq[Int] =
+        override def getParents(j: Int): Seq[Int] =
           if (j == i)
             0 until n
           else
@@ -73,7 +74,7 @@ class CollectMatricesRDD(@transient var bms: IndexedSeq[BlockMatrix])
       }
     }
 
-  def compute(split: Partition, context: TaskContext): Iterator[BDM[Double]] = {
+  override def compute(split: Partition, context: TaskContext): Iterator[BDM[Double]] = {
     val p = split.asInstanceOf[CollectMatricesRDDPartition]
     val m = BDM.zeros[Double](p.nRows, p.nCols)
     val prev = parent[((Int, Int), BDM[Double])](p.index)
@@ -117,11 +118,13 @@ object BlockMatrix {
       new RDD[((Int, Int), BDM[Double])](SparkBackend.sparkContext, Nil) {
         override val partitioner = Some(gp)
 
-        protected def getPartitions: Array[Partition] = Array.tabulate(gp.numPartitions)(pi =>
-          new Partition { def index: Int = pi }
-        )
+        override protected def getPartitions: Array[Partition] =
+          Array.tabulate(gp.numPartitions)(pi =>
+            new Partition { override def index: Int = pi }
+          )
 
-        def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] =
+        override def compute(split: Partition, context: TaskContext)
+          : Iterator[((Int, Int), BDM[Double])] =
           Iterator.single(piBlock(gp, split.index))
       },
       gp.blockSize,
@@ -203,7 +206,7 @@ object BlockMatrix {
 
   def readMetadata(fs: FS, uri: String): BlockMatrixMetadata =
     using(fs.open(uri + metadataRelativePath)) { is =>
-      implicit val formats = defaultJSONFormats
+      implicit val formats = DefaultFormats
       jackson.Serialization.read[BlockMatrixMetadata](is)
     }
 
@@ -483,7 +486,7 @@ object BlockMatrix {
       val fileData = numberedPartFiles.map { case (partFileName, _) => partFileName }
       val metadataPath = blockMatrixURI(rddIndex.toInt) + metadataRelativePath
       using(new DataOutputStream(fs.create(metadataPath))) { os =>
-        implicit val formats = defaultJSONFormats
+        implicit val formats = DefaultFormats
         val (blockSize, nRows, nCols, maybeBlocks) = blockMatrixMetadataFields(rddIndex.toInt)
         jackson.Serialization.write(
           BlockMatrixMetadata(blockSize, nRows, nCols, maybeBlocks, fileData.map(_.path)),
@@ -736,7 +739,7 @@ class BlockMatrix(
   ): Unit = {
 
     val writeRectangleBinary = (uos: OutputStream, dm: BDM[Double]) => {
-      val os = new DoubleOutputBuffer(uos, RichArray.defaultBufSize)
+      val os = new DoubleOutputBuffer(uos, ArrayImpex.DefaultBuffSize)
       os.writeDoubles(dm.t.toArray)
       os.close()
     }
@@ -1018,7 +1021,7 @@ class BlockMatrix(
     val fileData = blocks.writePartitions(ctx, uri, stageLocally, writeBlock)
 
     using(new DataOutputStream(fs.create(uri + metadataRelativePath))) { os =>
-      implicit val formats = defaultJSONFormats
+      implicit val formats = DefaultFormats
       jackson.Serialization.write(
         BlockMatrixMetadata(
           blockSize,
@@ -1159,12 +1162,12 @@ class BlockMatrix(
     val newBlocks =
       blocks.zipPartitions(that.blocks, preservesPartitioning = true) { (thisIter, thatIter) =>
         new Iterator[((Int, Int), BDM[Double])] {
-          def hasNext: Boolean = {
+          override def hasNext: Boolean = {
             assert(thisIter.hasNext == thatIter.hasNext)
             thisIter.hasNext
           }
 
-          def next(): ((Int, Int), BDM[Double]) = {
+          override def next(): ((Int, Int), BDM[Double]) = {
             val ((i1, j1), lm1) = thisIter.next()
             val ((i2, j2), lm2) = thatIter.next()
             assertCompatibleLocalMatrix(lm1)
@@ -1212,12 +1215,12 @@ class BlockMatrix(
     val newBlocks =
       blocks.zipPartitions(that.blocks, preservesPartitioning = true) { (thisIter, thatIter) =>
         new Iterator[((Int, Int), BDM[Double])] {
-          def hasNext: Boolean = {
+          override def hasNext: Boolean = {
             assert(thisIter.hasNext == thatIter.hasNext)
             thisIter.hasNext
           }
 
-          def next(): ((Int, Int), BDM[Double]) = {
+          override def next(): ((Int, Int), BDM[Double]) = {
             val ((i1, j1), lm1) = thisIter.next()
             val ((i2, j2), lm2) = thatIter.next()
             assertCompatibleLocalMatrix(lm1)
@@ -1276,14 +1279,14 @@ class BlockMatrix(
       blocks.zipPartitions(bm2.blocks, bm3.blocks, bm4.blocks, preservesPartitioning = true) {
         (it1, it2, it3, it4) =>
           new Iterator[((Int, Int), BDM[Double])] {
-            def hasNext: Boolean = {
+            override def hasNext: Boolean = {
               assert(it1.hasNext == it2.hasNext)
               assert(it1.hasNext == it3.hasNext)
               assert(it1.hasNext == it4.hasNext)
               it1.hasNext
             }
 
-            def next(): ((Int, Int), BDM[Double]) = {
+            override def next(): ((Int, Int), BDM[Double]) = {
               val ((i1, j1), lm1) = it1.next()
               val ((i2, j2), lm2) = it2.next()
               val ((i3, j3), lm3) = it3.next()
@@ -1380,12 +1383,12 @@ class BlockMatrix(
     val newBlocks =
       blocks.zipPartitions(that.blocks, preservesPartitioning = true) { (thisIter, thatIter) =>
         new Iterator[((Int, Int), BDM[Double])] {
-          def hasNext: Boolean = {
+          override def hasNext: Boolean = {
             assert(thisIter.hasNext == thatIter.hasNext)
             thisIter.hasNext
           }
 
-          def next(): ((Int, Int), BDM[Double]) = {
+          override def next(): ((Int, Int), BDM[Double]) = {
             val ((i1, j1), lm1) = thisIter.next()
             val ((i2, j2), lm2) = thatIter.next()
             assert(i1 == i2, s"$i1 $i2")
@@ -1511,7 +1514,8 @@ class BlockMatrix(
 
         for (k <- 0 until lm.rows)
           yield (k + iOffset, (jOffset, lm(k, ::).inner.toArray))
-      }.aggregateByKey(new Array[Double](nColsInt))(seqOp, combOp)
+      }
+        .aggregateByKey(new Array[Double](nColsInt))(seqOp, combOp)
         .map { case (i, a) => IndexedRow(i.toLong, BDV(a)) },
       nRows,
       nColsInt,
@@ -1697,7 +1701,7 @@ private class BlockMatrixFilterRDD(bm: BlockMatrix, keepRows: Array[Long], keepC
     s"Finished constructing block matrix filter RDD. Total time ${(System.nanoTime() - t0).toDouble / 1000000000}"
   )
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     Array.tabulate(newGP.numPartitions) { partitionIndex =>
       val blockIndex = newGP.partitionToBlock(partitionIndex)
       BlockMatrixFilterRDDPartition(
@@ -1709,7 +1713,7 @@ private class BlockMatrixFilterRDD(bm: BlockMatrix, keepRows: Array[Long], keepC
 
   override def getDependencies: Seq[Dependency[_]] = Array[Dependency[_]](
     new NarrowDependency(bm.blocks) {
-      def getParents(partitionId: Int): Seq[Int] = {
+      override def getParents(partitionId: Int): Seq[Int] = {
         val blockForPartition = newGP.partitionToBlock(partitionId)
         val blockParents = blockParentMap(blockForPartition)
         val partitionParents =
@@ -1719,7 +1723,8 @@ private class BlockMatrixFilterRDD(bm: BlockMatrix, keepRows: Array[Long], keepC
     }
   )
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val part = split.asInstanceOf[BlockMatrixFilterRDDPartition]
 
     val blockForPartition = newGP.partitionToBlock(split.index)
@@ -1831,7 +1836,7 @@ private class BlockMatrixFilterColsRDD(bm: BlockMatrix, keep: Array[Long])
 
   private val newGP = tempDenseGP.copy(partitionIndexToBlockIndex = newGPMaybeBlocks)
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     Array.tabulate(newGP.numPartitions) { partitionIndex: Int =>
       val blockIndex = newGP.partitionToBlock(partitionIndex)
       BlockMatrixFilterOneDimRDDPartition(
@@ -1842,7 +1847,7 @@ private class BlockMatrixFilterColsRDD(bm: BlockMatrix, keep: Array[Long])
 
   override def getDependencies: Seq[Dependency[_]] = Array[Dependency[_]](
     new NarrowDependency(bm.blocks) {
-      def getParents(partitionId: Int): Seq[Int] = {
+      override def getParents(partitionId: Int): Seq[Int] = {
         val blockForPartition = newGP.partitionToBlock(partitionId)
         val blockParents = blockParentMap(blockForPartition)
         val partitionParents =
@@ -1852,7 +1857,8 @@ private class BlockMatrixFilterColsRDD(bm: BlockMatrix, keep: Array[Long])
     }
   )
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val blockIndex = newGP.partitionToBlock(split.index)
     val (blockRow, newBlockCol) = newGP.blockCoordinates(blockIndex)
     val (blockNRows, newBlockNCols) = newGP.blockDims(blockIndex)
@@ -1934,7 +1940,7 @@ private class BlockMatrixFilterRowsRDD(bm: BlockMatrix, keep: Array[Long])
 
   private val newGP = tempDenseGP.copy(partitionIndexToBlockIndex = newGPMaybeBlocks)
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     Array.tabulate(newGP.numPartitions) { partitionIndex: Int =>
       val blockIndex = newGP.partitionToBlock(partitionIndex)
       BlockMatrixFilterOneDimRDDPartition(
@@ -1945,17 +1951,18 @@ private class BlockMatrixFilterRowsRDD(bm: BlockMatrix, keep: Array[Long])
 
   override def getDependencies: Seq[Dependency[_]] = Array[Dependency[_]](
     new NarrowDependency(bm.blocks) {
-      def getParents(partitionId: Int): Seq[Int] = {
+      override def getParents(partitionId: Int): Seq[Int] = {
         val blockForPartition = newGP.partitionToBlock(partitionId)
         val blockParents = blockParentMap(blockForPartition)
         val partitionParents =
-          blockParents.map(blockId => originalGP.blockToPartition(blockId)).toSet.toArray.sorted
+          blockParents.map(blockId => originalGP.blockToPartition(blockId)).distinct.sorted
         partitionParents
       }
     }
   )
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val blockIndex = newGP.partitionToBlock(split.index)
     val (newBlockRow, blockCol) = newGP.blockCoordinates(blockIndex)
     val (newBlockNRows, blockNCols) = newGP.blockDims(blockIndex)
@@ -2005,7 +2012,7 @@ private class BlockMatrixTransposeRDD(bm: BlockMatrix)
 
   override def getDependencies: Seq[Dependency[_]] = Array[Dependency[_]](
     new NarrowDependency(bm.blocks) {
-      def getParents(partitionId: Int): Seq[Int] = {
+      override def getParents(partitionId: Int): Seq[Int] = {
         val parent = transposedPartitionIndicesToParentPartitions(partitionId)
         val (oldI, oldJ) = bm.gp.partCoordinates(parent)
         val (newI, newJ) = newGP.partCoordinates(partitionId)
@@ -2015,11 +2022,12 @@ private class BlockMatrixTransposeRDD(bm: BlockMatrix)
     }
   )
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] =
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] =
     bm.blocks.iterator(split.asInstanceOf[BlockMatrixTransposeRDDPartition].prevPartition, context)
       .map { case ((j, i), lm) => ((i, j), lm.t) }
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     Array.tabulate(newGP.numPartitions) { pi =>
       BlockMatrixTransposeRDDPartition(
         pi,
@@ -2052,24 +2060,25 @@ private class BlockMatrixUnionOpRDD(
   override def getDependencies: Seq[Dependency[_]] =
     Array[Dependency[_]](
       new NarrowDependency(l.blocks) {
-        def getParents(partitionId: Int): Seq[Int] =
+        override def getParents(partitionId: Int): Seq[Int] =
           Array(lGP.blockToPartition(gp.partitionToBlock(partitionId))).filter(_ >= 0)
       },
       new NarrowDependency(r.blocks) {
-        def getParents(partitionId: Int): Seq[Int] =
+        override def getParents(partitionId: Int): Seq[Int] =
           Array(rGP.blockToPartition(gp.partitionToBlock(partitionId))).filter(_ >= 0)
       },
     )
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val (i, j) = gp.partCoordinates(split.index)
     val lm = op(block(l, lParts, lGP, context, i, j) -> block(r, rParts, rGP, context, i, j))
 
     Iterator.single(((i, j), lm))
   }
 
-  protected def getPartitions: Array[Partition] = Array.tabulate(gp.numPartitions)(pi =>
-    new Partition { def index: Int = pi }
+  override protected def getPartitions: Array[Partition] = Array.tabulate(gp.numPartitions)(pi =>
+    new Partition { override def index: Int = pi }
   )
 
   @transient override val partitioner: Option[Partitioner] = Some(gp)
@@ -2101,13 +2110,13 @@ private class BlockMatrixMultiplyRDD(l: BlockMatrix, r: BlockMatrix)
   override def getDependencies: Seq[Dependency[_]] =
     Array[Dependency[_]](
       new NarrowDependency(l.blocks) {
-        def getParents(partitionId: Int): Seq[Int] = {
+        override def getParents(partitionId: Int): Seq[Int] = {
           val i = gp.blockBlockRow(partitionId)
           (0 until nProducts).map(k => lGP.coordinatesPart(i, k)).filter(_ >= 0).to(ArraySeq)
         }
       },
       new NarrowDependency(r.blocks) {
-        def getParents(partitionId: Int): Seq[Int] = {
+        override def getParents(partitionId: Int): Seq[Int] = {
           val j = gp.blockBlockCol(partitionId)
           (0 until nProducts).map(k => rGP.coordinatesPart(k, j)).filter(_ >= 0).to(ArraySeq)
         }
@@ -2143,7 +2152,8 @@ private class BlockMatrixMultiplyRDD(l: BlockMatrix, r: BlockMatrix)
     )
   }
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val (i, j) = gp.blockCoordinates(split.index)
     val (blockNRows, blockNCols) = gp.blockDims(split.index)
     val product = BDM.zeros[Double](blockNRows, blockNCols)
@@ -2159,8 +2169,8 @@ private class BlockMatrixMultiplyRDD(l: BlockMatrix, r: BlockMatrix)
     Iterator.single(((i, j), product))
   }
 
-  protected def getPartitions: Array[Partition] = Array.tabulate(gp.numPartitions)(pi =>
-    new Partition { def index: Int = pi }
+  override protected def getPartitions: Array[Partition] = Array.tabulate(gp.numPartitions)(pi =>
+    new Partition { override def index: Int = pi }
   )
 
   @transient override val partitioner: Option[Partitioner] = Some(gp)
@@ -2258,12 +2268,12 @@ class WriteBlocksRDD(
   override def getDependencies: Seq[Dependency[_]] =
     Array[Dependency[_]](
       new NarrowDependency(crdd.rdd) {
-        def getParents(partitionId: Int): Seq[Int] =
+        override def getParents(partitionId: Int): Seq[Int] =
           partitions(partitionId).asInstanceOf[WriteBlocksRDDPartition].range
       }
     )
 
-  protected def getPartitions: Array[Partition] = {
+  override protected def getPartitions: Array[Partition] = {
     val nRows = parentPartStarts.last
     assert(nRows == gp.nRows)
     val nBlockRows = gp.nBlockRows
@@ -2304,7 +2314,7 @@ class WriteBlocksRDD(
     parts
   }
 
-  def compute(split: Partition, context: TaskContext): Iterator[(Int, String)] = {
+  override def compute(split: Partition, context: TaskContext): Iterator[(Int, String)] = {
     val blockRow = split.index
     val nRowsInBlock = gp.blockRowNRows(blockRow)
     val ctx = TaskContext.get()
diff --git a/hail/hail/src/is/hail/linalg/GridPartitioner.scala b/hail/hail/src/is/hail/linalg/GridPartitioner.scala
index 1b6cc1a4d05..e3031d428fc 100644
--- a/hail/hail/src/is/hail/linalg/GridPartitioner.scala
+++ b/hail/hail/src/is/hail/linalg/GridPartitioner.scala
@@ -1,5 +1,6 @@
 package is.hail.linalg
 
+import is.hail.collection.implicits.toRichOrderedSeq
 import is.hail.utils._
 
 import scala.collection.mutable
diff --git a/hail/hail/src/is/hail/linalg/LAPACK.scala b/hail/hail/src/is/hail/linalg/LAPACK.scala
index 2b1a1095a90..ffa9f63fbda 100644
--- a/hail/hail/src/is/hail/linalg/LAPACK.scala
+++ b/hail/hail/src/is/hail/linalg/LAPACK.scala
@@ -19,7 +19,7 @@ class UnderscoreFunctionMapper extends FunctionMapper {
 // see: https://software.intel.com/content/www/us/en/develop/documentation/mkl-linux-developer-guide/top/language-specific-usage-options/mixed-language-programming-with-the-intel-math-kernel-library/calling-lapack-blas-and-cblas-routines-from-c-c-language-environments.html
 object LAPACK extends Logging {
   private[this] val libraryInstance = ThreadLocal.withInitial(new Supplier[LAPACKLibrary]() {
-    def get() = {
+    override def get() = {
       val mklEnvVar = "HAIL_MKL_PATH"
       val openblasEnvVar = "HAIL_OPENBLAS_PATH"
       val libraryName = if (sys.env.contains(mklEnvVar)) {
diff --git a/hail/hail/src/is/hail/linalg/MatrixSparsity.scala b/hail/hail/src/is/hail/linalg/MatrixSparsity.scala
index 9030f7a68f1..33777707206 100644
--- a/hail/hail/src/is/hail/linalg/MatrixSparsity.scala
+++ b/hail/hail/src/is/hail/linalg/MatrixSparsity.scala
@@ -1,8 +1,8 @@
 package is.hail.linalg
 
-import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.collection.compat._
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichOrderedSeq
 
 import scala.collection.Searching._
 import scala.collection.compat._
@@ -126,7 +126,7 @@ object MatrixSparsity {
       }
     }
 
-    def newToOldPosNonSubset(newSparsity: Sparse): IndexedSeq[Integer] = {
+    override def newToOldPosNonSubset(newSparsity: Sparse): IndexedSeq[Integer] = {
       if (newSparsity.isEmpty) return ArraySeq.empty
       var cur =
         definedCoords.search(newSparsity.definedCoords.head)(Ordering.by(_.swap)).insertionPoint
diff --git a/hail/hail/src/is/hail/linalg/RowMatrix.scala b/hail/hail/src/is/hail/linalg/RowMatrix.scala
index a58ea3634d9..4ef5d4877dd 100644
--- a/hail/hail/src/is/hail/linalg/RowMatrix.scala
+++ b/hail/hail/src/is/hail/linalg/RowMatrix.scala
@@ -5,6 +5,7 @@ import is.hail.backend.spark.SparkBackend
 import is.hail.io.InputBuffer
 import is.hail.io.fs.FS
 import is.hail.rvd.RVDPartitioner
+import is.hail.sparkextras.implicits._
 import is.hail.types.virtual.{TInt64, TStruct}
 import is.hail.utils._
 
@@ -303,11 +304,12 @@ class ReadBlocksAsRowsRDD(
   private val nBlockCols = gp.nBlockCols
   private val blockSize = gp.blockSize
 
-  protected def getPartitions: Array[Partition] = Array.tabulate(partitionStarts.length - 1)(pi =>
-    ReadBlocksAsRowsRDDPartition(pi, partitionStarts(pi), partitionStarts(pi + 1))
-  )
+  override protected def getPartitions: Array[Partition] =
+    Array.tabulate(partitionStarts.length - 1)(pi =>
+      ReadBlocksAsRowsRDDPartition(pi, partitionStarts(pi), partitionStarts(pi + 1))
+    )
 
-  def compute(split: Partition, context: TaskContext): Iterator[(Long, Array[Double])] = {
+  override def compute(split: Partition, context: TaskContext): Iterator[(Long, Array[Double])] = {
     val ReadBlocksAsRowsRDDPartition(_, start, end) =
       split.asInstanceOf[ReadBlocksAsRowsRDDPartition]
 
@@ -315,9 +317,9 @@ class ReadBlocksAsRowsRDD(
     var i = start
 
     new Iterator[(Long, Array[Double])] {
-      def hasNext: Boolean = i < end
+      override def hasNext: Boolean = i < end
 
-      def next(): (Long, Array[Double]) = {
+      override def next(): (Long, Array[Double]) = {
         if (i == start || i % blockSize == 0) {
           val blockRow = (i / blockSize).toInt
           val nRowsInBlock = gp.blockRowNRows(blockRow)
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichDenseMatrixDouble.scala b/hail/hail/src/is/hail/linalg/implicits/RichDenseMatrixDouble.scala
similarity index 94%
rename from hail/hail/src/is/hail/utils/richUtils/RichDenseMatrixDouble.scala
rename to hail/hail/src/is/hail/linalg/implicits/RichDenseMatrixDouble.scala
index 1d36dee6cac..9fae2f3a690 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichDenseMatrixDouble.scala
+++ b/hail/hail/src/is/hail/linalg/implicits/RichDenseMatrixDouble.scala
@@ -1,6 +1,7 @@
-package is.hail.utils.richUtils
+package is.hail.linalg.implicits
 
 import is.hail.backend.ExecuteContext
+import is.hail.expr.ir.partFile
 import is.hail.io._
 import is.hail.io.fs.FS
 import is.hail.linalg.{BlockMatrix, BlockMatrixMetadata, GridPartitioner}
@@ -11,7 +12,7 @@ import scala.collection.parallel.CollectionConverters._
 import java.io.{DataInputStream, DataOutputStream, InputStream, OutputStream}
 
 import breeze.linalg.{DenseMatrix => BDM}
-import org.json4s.jackson
+import org.json4s.{jackson, DefaultFormats}
 
 object RichDenseMatrixDouble {
   def apply(nRows: Int, nCols: Int, data: Array[Double], isTranspose: Boolean = false)
@@ -55,7 +56,7 @@ object RichDenseMatrixDouble {
   def importFromDoubles(fs: FS, path: String, nRows: Int, nCols: Int, rowMajor: Boolean)
     : BDM[Double] = {
     require(nRows * nCols.toLong <= Int.MaxValue)
-    val data = RichArray.importFromDoubles(fs, path, nRows * nCols)
+    val data = ArrayImpex.importFromDoubles(fs, path, nRows * nCols)
 
     RichDenseMatrixDouble(nRows, nCols, data, rowMajor)
   }
@@ -64,7 +65,7 @@ object RichDenseMatrixDouble {
     val (data, rowMajor) = m.toCompactData(forceRowMajor)
     assert(data.length == m.rows * m.cols)
 
-    RichArray.exportToDoubles(fs, path, data)
+    ArrayImpex.exportToDoubles(fs, path, data)
 
     rowMajor
   }
@@ -157,7 +158,7 @@ class RichDenseMatrixDouble(val m: BDM[Double]) extends AnyVal {
       .toArray
 
     using(new DataOutputStream(fs.create(path + BlockMatrix.metadataRelativePath))) { os =>
-      implicit val formats = defaultJSONFormats
+      implicit val formats = DefaultFormats
       jackson.Serialization.write(
         BlockMatrixMetadata(
           blockSize,
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichIndexedRowMatrix.scala b/hail/hail/src/is/hail/linalg/implicits/RichIndexedRowMatrix.scala
similarity index 93%
rename from hail/hail/src/is/hail/utils/richUtils/RichIndexedRowMatrix.scala
rename to hail/hail/src/is/hail/linalg/implicits/RichIndexedRowMatrix.scala
index 65cd8f16dca..8e1d0f385f2 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichIndexedRowMatrix.scala
+++ b/hail/hail/src/is/hail/linalg/implicits/RichIndexedRowMatrix.scala
@@ -1,7 +1,7 @@
-package is.hail.utils.richUtils
+package is.hail.linalg.implicits
 
 import is.hail.linalg._
-import is.hail.utils._
+import is.hail.sparkextras.implicits._
 
 import breeze.linalg.{DenseMatrix => BDM}
 import org.apache.spark._
@@ -85,7 +85,8 @@ private class EmptyPartitionIsAZeroMatrixRDD(blocks: RDD[((Int, Int), BDM[Double
     case Some(p: GridPartitioner) => p
   }
 
-  def compute(split: Partition, context: TaskContext): Iterator[((Int, Int), BDM[Double])] = {
+  override def compute(split: Partition, context: TaskContext)
+    : Iterator[((Int, Int), BDM[Double])] = {
     val p = split.asInstanceOf[BlockPartition]
     val it = blocks.iterator(split, context)
     if (it.hasNext)
@@ -94,7 +95,7 @@ private class EmptyPartitionIsAZeroMatrixRDD(blocks: RDD[((Int, Int), BDM[Double
       Iterator.single(p.blockCoordinates -> BDM.zeros[Double](p.blockDims._1, p.blockDims._2))
   }
 
-  protected def getPartitions: Array[Partition] =
+  override protected def getPartitions: Array[Partition] =
     blocks.partitions.map { p =>
       new BlockPartition(p.index, gp.blockCoordinates(p.index), gp.blockDims(p.index))
     }.toArray
diff --git a/hail/hail/src/is/hail/linalg/implicits/package.scala b/hail/hail/src/is/hail/linalg/implicits/package.scala
new file mode 100644
index 00000000000..5fc99305ae3
--- /dev/null
+++ b/hail/hail/src/is/hail/linalg/implicits/package.scala
@@ -0,0 +1,58 @@
+package is.hail.linalg
+
+import _root_.breeze.linalg.operators.{OpAdd, OpSub}
+import breeze.{linalg => breeze}
+import org.apache.spark.mllib.{linalg => spark}
+import org.apache.spark.mllib.linalg.distributed.{IndexedRow, IndexedRowMatrix}
+
+package object implicits {
+  implicit def toRichDenseMatrixDouble(m: breeze.DenseMatrix[Double]): RichDenseMatrixDouble =
+    new RichDenseMatrixDouble(m)
+
+  implicit def toRichIndexedRowMatrix(irm: IndexedRowMatrix): RichIndexedRowMatrix =
+    new RichIndexedRowMatrix(irm)
+
+  implicit def sparkToBreezeDenseVector(v: spark.DenseVector): breeze.DenseVector[Double] =
+    new breeze.DenseVector(v.values)
+
+  implicit def sparkToBreezeSparseVector(v: spark.SparseVector): breeze.SparseVector[Double] =
+    new breeze.SparseVector(v.indices, v.values, v.size)
+
+  implicit def sparkToBreezeVector(v: spark.Vector): breeze.Vector[Double] =
+    v match {
+      case v: spark.SparseVector => v
+      case v: spark.DenseVector => v
+    }
+
+  implicit def breezeToSparkDenseVector(v: breeze.DenseVector[Double]): spark.DenseVector =
+    new spark.DenseVector(v.toArray)
+
+  implicit def breezeToSparkSparseVector(v: breeze.SparseVector[Double]): spark.SparseVector =
+    new spark.SparseVector(v.length, v.array.index, v.array.data)
+
+  implicit def breezeToSparkVector(v: breeze.Vector[Double]): spark.Vector =
+    v match {
+      case v: breeze.DenseVector[Double] => v
+      case v: breeze.SparseVector[Double] => v
+    }
+
+  implicit lazy val subBVectorSVector
+    : OpSub.Impl2[breeze.Vector[Double], spark.Vector, breeze.Vector[Double]] =
+    (a: breeze.Vector[Double], b: spark.Vector) =>
+      a - sparkToBreezeVector(b)
+
+  implicit lazy val subBVectorIndexedRow
+    : OpSub.Impl2[breeze.Vector[Double], IndexedRow, IndexedRow] =
+    (a: breeze.Vector[Double], b: IndexedRow) =>
+      IndexedRow(b.index, a - sparkToBreezeVector(b.vector))
+
+  implicit lazy val addBVectorSVector
+    : OpAdd.Impl2[breeze.Vector[Double], spark.Vector, breeze.Vector[Double]] =
+    (a: breeze.Vector[Double], b: spark.Vector) =>
+      a + sparkToBreezeVector(b)
+
+  implicit lazy val addBVectorIndexedRow
+    : OpAdd.Impl2[breeze.Vector[Double], IndexedRow, IndexedRow] =
+    (a: breeze.Vector[Double], b: IndexedRow) =>
+      IndexedRow(b.index, a + sparkToBreezeVector(b.vector))
+}
diff --git a/hail/hail/src/is/hail/linalg/package.scala b/hail/hail/src/is/hail/linalg/package.scala
index 59a6620ccbb..0403e941e56 100644
--- a/hail/hail/src/is/hail/linalg/package.scala
+++ b/hail/hail/src/is/hail/linalg/package.scala
@@ -13,4 +13,5 @@ package object linalg {
     ]].register(
       DenseMatrix.implOpMulMatrix_DMD_DVD_eq_DVD
     )
+
 }
diff --git a/hail/hail/src/is/hail/lir/Blocks.scala b/hail/hail/src/is/hail/lir/Blocks.scala
index f7bee6bb757..0b3c2602fc4 100644
--- a/hail/hail/src/is/hail/lir/Blocks.scala
+++ b/hail/hail/src/is/hail/lir/Blocks.scala
@@ -11,9 +11,9 @@ class Blocks(
 
   def nBlocks: Int = blocks.length
 
-  def length: Int = blocks.length
+  override def length: Int = blocks.length
 
-  def apply(i: Int): Block = blocks(i)
+  override def apply(i: Int): Block = blocks(i)
 
   def index(block: Block): Int = blockIdx.get(block)
 }
diff --git a/hail/hail/src/is/hail/lir/Emit.scala b/hail/hail/src/is/hail/lir/Emit.scala
index 033350a9006..b8584f002b3 100644
--- a/hail/hail/src/is/hail/lir/Emit.scala
+++ b/hail/hail/src/is/hail/lir/Emit.scala
@@ -1,6 +1,7 @@
 package is.hail.lir
 
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.collection.mutable
 
diff --git a/hail/hail/src/is/hail/lir/Locals.scala b/hail/hail/src/is/hail/lir/Locals.scala
index 5e2ed36ee44..45e81c6f0f9 100644
--- a/hail/hail/src/is/hail/lir/Locals.scala
+++ b/hail/hail/src/is/hail/lir/Locals.scala
@@ -7,9 +7,9 @@ class Locals(
 
   def nLocals: Int = locals.length
 
-  def length: Int = locals.length
+  override def length: Int = locals.length
 
-  def apply(i: Int): Local = locals(i)
+  override def apply(i: Int): Local = locals(i)
 
   def getIndex(l: Local): Option[Int] = {
     l match {
diff --git a/hail/hail/src/is/hail/lir/PST.scala b/hail/hail/src/is/hail/lir/PST.scala
index f8f4eec3f4d..ab1b9334244 100644
--- a/hail/hail/src/is/hail/lir/PST.scala
+++ b/hail/hail/src/is/hail/lir/PST.scala
@@ -1,6 +1,6 @@
 package is.hail.lir
 
-import is.hail.expr.ir.{BooleanArrayBuilder, IntArrayBuilder}
+import is.hail.collection.{BooleanArrayBuilder, IntArrayBuilder}
 
 import scala.collection.mutable
 
diff --git a/hail/hail/src/is/hail/lir/SplitMethod.scala b/hail/hail/src/is/hail/lir/SplitMethod.scala
index e775655d240..1e948af07e6 100644
--- a/hail/hail/src/is/hail/lir/SplitMethod.scala
+++ b/hail/hail/src/is/hail/lir/SplitMethod.scala
@@ -1,6 +1,7 @@
 package is.hail.lir
 
 import is.hail.asm4s.{classInfo, BooleanInfo, IntInfo, UnitInfo}
+import is.hail.collection.FastSeq
 import is.hail.utils._
 
 import scala.collection.mutable
diff --git a/hail/hail/src/is/hail/lir/X.scala b/hail/hail/src/is/hail/lir/X.scala
index b7b5965af9a..cf0578e1c6b 100644
--- a/hail/hail/src/is/hail/lir/X.scala
+++ b/hail/hail/src/is/hail/lir/X.scala
@@ -3,7 +3,9 @@ package is.hail.lir
 import is.hail.asm4s.{
   arrayInfo, ByteInfo, ClassInfo, DoubleInfo, FloatInfo, IntInfo, LongInfo, TypeInfo,
 }
+import is.hail.collection.ObjectArrayStack
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.collection.mutable
 
@@ -137,12 +139,12 @@ abstract class FieldRef {
 
 class Field private[lir] (classx: Classx[_], val name: String, val ti: TypeInfo[_])
     extends FieldRef {
-  def owner: String = classx.name
+  override def owner: String = classx.name
 }
 
 class StaticField private[lir] (classx: Classx[_], val name: String, val ti: TypeInfo[_])
     extends FieldRef {
-  def owner: String = classx.name
+  override def owner: String = classx.name
 }
 
 class FieldLit(
@@ -176,11 +178,11 @@ class Method private[lir] (
 
   def nParameters: Int = parameterTypeInfo.length + (!isStatic).toInt
 
-  def owner: String = classx.name
+  override def owner: String = classx.name
 
-  def desc = s"(${parameterTypeInfo.map(_.desc).mkString})${returnTypeInfo.desc}"
+  override def desc = s"(${parameterTypeInfo.map(_.desc).mkString})${returnTypeInfo.desc}"
 
-  def isInterface: Boolean = false
+  override def isInterface: Boolean = false
 
   private var _entry: Block = _
 
@@ -520,7 +522,7 @@ abstract class StmtX extends X {
   var prev: StmtX = _
   var next: StmtX = _
 
-  def remove(): Unit = {
+  override def remove(): Unit = {
     assert(parent != null)
     if (parent.first == this)
       parent.first = next
@@ -602,7 +604,7 @@ abstract class ValueX extends X {
 
   def ti: TypeInfo[_]
 
-  def remove(): Unit = {
+  override def remove(): Unit = {
     var i = 0
     while (parent.children(i) ne this)
       i += 1
@@ -626,14 +628,14 @@ class GotoX(var lineNumber: Int = 0) extends ControlX {
 
   def setL(newL: Block): Unit = setTarget(0, newL)
 
-  def targetArity(): Int = 1
+  override def targetArity(): Int = 1
 
-  def target(i: Int): Block = {
+  override def target(i: Int): Block = {
     assert(i == 0)
     _L
   }
 
-  def setTarget(i: Int, b: Block): Unit = {
+  override def setTarget(i: Int, b: Block): Unit = {
     assert(i == 0)
     if (_L != null)
       _L.removeUse(this, 0)
@@ -655,9 +657,9 @@ class IfX(val op: Int, var lineNumber: Int = 0) extends ControlX {
 
   def setLfalse(newLfalse: Block): Unit = setTarget(1, newLfalse)
 
-  def targetArity(): Int = 2
+  override def targetArity(): Int = 2
 
-  def target(i: Int): Block = {
+  override def target(i: Int): Block = {
     if (i == 0)
       _Ltrue
     else {
@@ -666,7 +668,7 @@ class IfX(val op: Int, var lineNumber: Int = 0) extends ControlX {
     }
   }
 
-  def setTarget(i: Int, b: Block): Unit = {
+  override def setTarget(i: Int, b: Block): Unit = {
     if (i == 0) {
       if (_Ltrue != null)
         _Ltrue.removeUse(this, 0)
@@ -706,15 +708,15 @@ class SwitchX(var lineNumber: Int = 0) extends ControlX {
       if (block != null) block.addUse(this, i + 1)
   }
 
-  def targetArity(): Int = 1 + _Lcases.length
+  override def targetArity(): Int = 1 + _Lcases.length
 
-  def target(i: Int): Block =
+  override def target(i: Int): Block =
     if (i == 0)
       _Ldefault
     else
       _Lcases(i - 1)
 
-  def setTarget(i: Int, b: Block): Unit = {
+  override def setTarget(i: Int, b: Block): Unit = {
     if (i == 0) {
       if (_Ldefault != null)
         _Ldefault.removeUse(this, 0)
@@ -739,19 +741,19 @@ class PutFieldX(val op: Int, val f: FieldRef, var lineNumber: Int = 0) extends S
 class IincX(var l: Local, val i: Int, var lineNumber: Int = 0) extends StmtX
 
 class ReturnX(var lineNumber: Int = 0) extends ControlX {
-  def targetArity(): Int = 0
+  override def targetArity(): Int = 0
 
-  def target(i: Int): Block = throw new IndexOutOfBoundsException()
+  override def target(i: Int): Block = throw new IndexOutOfBoundsException()
 
-  def setTarget(i: Int, b: Block): Unit = throw new IndexOutOfBoundsException()
+  override def setTarget(i: Int, b: Block): Unit = throw new IndexOutOfBoundsException()
 }
 
 class ThrowX(var lineNumber: Int = 0) extends ControlX {
-  def targetArity(): Int = 0
+  override def targetArity(): Int = 0
 
-  def target(i: Int): Block = throw new IndexOutOfBoundsException()
+  override def target(i: Int): Block = throw new IndexOutOfBoundsException()
 
-  def setTarget(i: Int, b: Block): Unit = throw new IndexOutOfBoundsException()
+  override def setTarget(i: Int, b: Block): Unit = throw new IndexOutOfBoundsException()
 }
 
 class StmtOpX(val op: Int, var lineNumber: Int = 0) extends StmtX
@@ -761,7 +763,7 @@ class MethodStmtX(val op: Int, val method: MethodRef, var lineNumber: Int = 0) e
 class TypeInsnX(val op: Int, val ti: TypeInfo[_], var lineNumber: Int = 0) extends ValueX {}
 
 class InsnX(val op: Int, _ti: TypeInfo[_], var lineNumber: Int = 0) extends ValueX {
-  def ti: TypeInfo[_] = {
+  override def ti: TypeInfo[_] = {
     if (_ti != null)
       return _ti
 
@@ -838,15 +840,15 @@ class InsnX(val op: Int, _ti: TypeInfo[_], var lineNumber: Int = 0) extends Valu
 }
 
 class LoadX(var l: Local, var lineNumber: Int = 0) extends ValueX {
-  def ti: TypeInfo[_] = l.ti
+  override def ti: TypeInfo[_] = l.ti
 }
 
 class GetFieldX(val op: Int, val f: FieldRef, var lineNumber: Int = 0) extends ValueX {
-  def ti: TypeInfo[_] = f.ti
+  override def ti: TypeInfo[_] = f.ti
 }
 
 class NewArrayX(val eti: TypeInfo[_], var lineNumber: Int = 0) extends ValueX {
-  def ti: TypeInfo[_] = arrayInfo(eti)
+  override def ti: TypeInfo[_] = arrayInfo(eti)
 }
 
 class NewInstanceX(val ti: TypeInfo[_], val ctor: MethodRef, var lineNumber: Int = 0) extends ValueX
@@ -861,5 +863,5 @@ class LdcX(val a: Any, val ti: TypeInfo[_], var lineNumber: Int = 0) extends Val
 }
 
 class MethodX(val op: Int, val method: MethodRef, var lineNumber: Int = 0) extends ValueX {
-  def ti: TypeInfo[_] = method.returnTypeInfo
+  override def ti: TypeInfo[_] = method.returnTypeInfo
 }
diff --git a/hail/hail/src/is/hail/lir/package.scala b/hail/hail/src/is/hail/lir/package.scala
index ed88fa9c109..84b1a71ad9c 100644
--- a/hail/hail/src/is/hail/lir/package.scala
+++ b/hail/hail/src/is/hail/lir/package.scala
@@ -3,7 +3,7 @@ package is.hail
 import is.hail.asm4s.{
   ArrayInfo, BooleanInfo, ClassInfo, DoubleInfo, FloatInfo, IntInfo, LongInfo, TypeInfo,
 }
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import org.objectweb.asm.Opcodes._
 
diff --git a/hail/hail/src/is/hail/methods/ForceCount.scala b/hail/hail/src/is/hail/methods/ForceCount.scala
index 522be2bbec6..b6c433d4dcf 100644
--- a/hail/hail/src/is/hail/methods/ForceCount.scala
+++ b/hail/hail/src/is/hail/methods/ForceCount.scala
@@ -9,7 +9,7 @@ import is.hail.types.virtual.{MatrixType, TInt64, TableType, Type}
 case class ForceCountTable() extends TableToValueFunction {
   override def typ(childType: TableType): Type = TInt64
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
 
   override def execute(ctx: ExecuteContext, tv: TableValue): Any = tv.rvd.count()
 }
@@ -17,7 +17,7 @@ case class ForceCountTable() extends TableToValueFunction {
 case class ForceCountMatrixTable() extends MatrixToValueFunction {
   override def typ(childType: MatrixType): Type = TInt64
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
 
   override def execute(ctx: ExecuteContext, mv: MatrixValue): Any =
     throw new UnsupportedOperationException
diff --git a/hail/hail/src/is/hail/methods/IBD.scala b/hail/hail/src/is/hail/methods/IBD.scala
index 792a0232840..35a23f19e0c 100644
--- a/hail/hail/src/is/hail/methods/IBD.scala
+++ b/hail/hail/src/is/hail/methods/IBD.scala
@@ -2,9 +2,12 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichOption
 import is.hail.expr.ir._
 import is.hail.expr.ir.functions.MatrixToTableFunction
 import is.hail.sparkextras.ContextRDD
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical.{PCanonicalString, PCanonicalStruct, PFloat64, PInt64}
 import is.hail.types.virtual.{MatrixType, TFloat64, TStruct, TableType}
 import is.hail.utils._
@@ -388,12 +391,12 @@ case class IBD(
     }
   }
 
-  def preservesPartitionCounts: Boolean = false
+  override def preservesPartitionCounts: Boolean = false
 
-  def typ(childType: MatrixType): TableType =
+  override def typ(childType: MatrixType): TableType =
     TableType(IBD.ibdPType.virtualType, IBD.ibdKey, TStruct.empty)
 
-  def execute(ctx: ExecuteContext, input: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, input: MatrixValue): TableValue = {
     input.requireUniqueSamples("ibd")
     val computeMaf = mafFieldName.map(IBD.generateComputeMaf(input, _))
     val crdd =
diff --git a/hail/hail/src/is/hail/methods/LinearRegression.scala b/hail/hail/src/is/hail/methods/LinearRegression.scala
index eed287388d8..7a69d390aa2 100644
--- a/hail/hail/src/is/hail/methods/LinearRegression.scala
+++ b/hail/hail/src/is/hail/methods/LinearRegression.scala
@@ -2,7 +2,9 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
-import is.hail.expr.ir.{IntArrayBuilder, MatrixValue, TableValue}
+import is.hail.collection.IntArrayBuilder
+import is.hail.collection.implicits.toRichIterator
+import is.hail.expr.ir.{MatrixValue, TableValue}
 import is.hail.expr.ir.functions.MatrixToTableFunction
 import is.hail.stats._
 import is.hail.types.physical.PStruct
@@ -39,9 +41,9 @@ case class LinearRegressionRowsSingle(
     )
   }
 
-  def preservesPartitionCounts: Boolean = true
+  override def preservesPartitionCounts: Boolean = true
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
     val (y, cov, completeColIdx) =
       RegressionUtils.getPhenosCovCompleteSamples(mv, yFields.toArray, covFields.toArray)
 
@@ -219,9 +221,9 @@ case class LinearRegressionRowsChained(
     )
   }
 
-  def preservesPartitionCounts: Boolean = true
+  override def preservesPartitionCounts: Boolean = true
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
 
     val localData = yFields.map(y =>
       RegressionUtils.getPhenosCovCompleteSamples(mv, y.toArray, covFields.toArray)
diff --git a/hail/hail/src/is/hail/methods/LocalLDPrune.scala b/hail/hail/src/is/hail/methods/LocalLDPrune.scala
index 12f87044d13..135e2033a5f 100644
--- a/hail/hail/src/is/hail/methods/LocalLDPrune.scala
+++ b/hail/hail/src/is/hail/methods/LocalLDPrune.scala
@@ -1,6 +1,7 @@
 package is.hail.methods
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.LongArrayBuilder
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs.{GetField, StreamLocalLDPrune, ToArray, ToStream}
 import is.hail.expr.ir.functions.MatrixToTableFunction
@@ -305,7 +306,7 @@ case class LocalLDPrune(
       globalType = TStruct.empty,
     )
 
-  def preservesPartitionCounts: Boolean = false
+  override def preservesPartitionCounts: Boolean = false
 
   def makeStream(stream: IR, entriesFieldName: String, nCols: IR): StreamLocalLDPrune = {
     val newRow = mapIR(stream) { row =>
@@ -318,7 +319,7 @@ case class LocalLDPrune(
     StreamLocalLDPrune(newRow, r2Threshold, windowSize, maxQueueSize, nCols)
   }
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
     val nSamples = mv.nCols
     val tableType = typ(mv.typ)
     val ts = TableExecuteIntermediate(mv.toTableValue).asTableStage(ctx).mapPartition(Some(
diff --git a/hail/hail/src/is/hail/methods/LocalWhitening.scala b/hail/hail/src/is/hail/methods/LocalWhitening.scala
index 770748491e5..c2cdb0e56db 100644
--- a/hail/hail/src/is/hail/methods/LocalWhitening.scala
+++ b/hail/hail/src/is/hail/methods/LocalWhitening.scala
@@ -2,11 +2,11 @@ package is.hail.methods
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCanonicalNDArray, PFloat64Required}
 import is.hail.types.physical.stypes.interfaces.{ColonIndex => Colon, _}
 import is.hail.types.physical.stypes.interfaces.SNDArray.assertColMajor
-import is.hail.utils.FastSeq
 
 class LocalWhitening(
   cb: EmitCodeBuilder,
diff --git a/hail/hail/src/is/hail/methods/LogisticRegression.scala b/hail/hail/src/is/hail/methods/LogisticRegression.scala
index e792e1d8d89..49e2919064b 100644
--- a/hail/hail/src/is/hail/methods/LogisticRegression.scala
+++ b/hail/hail/src/is/hail/methods/LogisticRegression.scala
@@ -2,7 +2,8 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
-import is.hail.expr.ir.{IntArrayBuilder, MatrixValue, TableValue}
+import is.hail.collection.IntArrayBuilder
+import is.hail.expr.ir.{MatrixValue, TableValue}
 import is.hail.expr.ir.functions.MatrixToTableFunction
 import is.hail.stats._
 import is.hail.types.virtual.{MatrixType, TArray, TFloat64, TStruct, TableType}
@@ -31,9 +32,9 @@ case class LogisticRegression(
     )
   }
 
-  def preservesPartitionCounts: Boolean = true
+  override def preservesPartitionCounts: Boolean = true
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
     val logRegTest = LogisticRegressionTest.tests(test)
     val tableType = typ(mv.typ)
     val newRVDType = tableType.canonicalRVDType
diff --git a/hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala b/hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala
index 58b00d092ab..eed54b2aa4e 100644
--- a/hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala
+++ b/hail/hail/src/is/hail/methods/MatrixExportEntriesByCol.scala
@@ -2,13 +2,14 @@ package is.hail.methods
 
 import is.hail.annotations.{UnsafeIndexedSeq, UnsafeRow}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.TableAnnotationImpex
-import is.hail.expr.ir.MatrixValue
+import is.hail.expr.ir.{partFile, MatrixValue}
 import is.hail.expr.ir.functions.MatrixToValueFunction
 import is.hail.types.{RTable, TypeWithRequiredness}
 import is.hail.types.virtual.{MatrixType, TVoid, Type}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import java.io.{BufferedOutputStream, OutputStreamWriter}
 
@@ -22,11 +23,11 @@ case class MatrixExportEntriesByCol(
   headerJsonInFile: Boolean,
   useStringKeyAsFileName: Boolean,
 ) extends MatrixToValueFunction with Logging {
-  def typ(childType: MatrixType): Type = TVoid
+  override def typ(childType: MatrixType): Type = TVoid
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): Any = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): Any = {
     val fs = ctx.fs
 
     fs.delete(path, recursive = true) // overwrite by default
diff --git a/hail/hail/src/is/hail/methods/NPartitions.scala b/hail/hail/src/is/hail/methods/NPartitions.scala
index 0f11da13751..e513411f4a8 100644
--- a/hail/hail/src/is/hail/methods/NPartitions.scala
+++ b/hail/hail/src/is/hail/methods/NPartitions.scala
@@ -9,7 +9,7 @@ import is.hail.types.virtual.{MatrixType, TInt32, TableType, Type}
 case class NPartitionsTable() extends TableToValueFunction {
   override def typ(childType: TableType): Type = TInt32
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
 
   override def execute(ctx: ExecuteContext, tv: TableValue): Any = tv.rvd.getNumPartitions
 }
@@ -17,7 +17,7 @@ case class NPartitionsTable() extends TableToValueFunction {
 case class NPartitionsMatrixTable() extends MatrixToValueFunction {
   override def typ(childType: MatrixType): Type = TInt32
 
-  def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
+  override def unionRequiredness(childType: RTable, resultType: TypeWithRequiredness): Unit = ()
 
   override def execute(ctx: ExecuteContext, mv: MatrixValue): Any = mv.rvd.getNumPartitions
 
diff --git a/hail/hail/src/is/hail/methods/Nirvana.scala b/hail/hail/src/is/hail/methods/Nirvana.scala
index db5ed39cd4b..a0b9a6d2c7b 100644
--- a/hail/hail/src/is/hail/methods/Nirvana.scala
+++ b/hail/hail/src/is/hail/methods/Nirvana.scala
@@ -2,6 +2,8 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterator
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir.TableValue
 import is.hail.expr.ir.functions.TableToTableFunction
@@ -504,8 +506,8 @@ case class Nirvana(config: String, blockSize: Int = 500000) extends TableToTable
     )
   }
 
-  def preservesPartitionCounts: Boolean = false
+  override def preservesPartitionCounts: Boolean = false
 
-  def execute(ctx: ExecuteContext, tv: TableValue): TableValue =
+  override def execute(ctx: ExecuteContext, tv: TableValue): TableValue =
     Nirvana.annotate(ctx, tv, config, blockSize)
 }
diff --git a/hail/hail/src/is/hail/methods/PCA.scala b/hail/hail/src/is/hail/methods/PCA.scala
index 13a5a74486f..da27ff06096 100644
--- a/hail/hail/src/is/hail/methods/PCA.scala
+++ b/hail/hail/src/is/hail/methods/PCA.scala
@@ -2,6 +2,8 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.{toRichIterable, toRichIterator}
 import is.hail.expr.ir.{MatrixValue, TableValue}
 import is.hail.expr.ir.functions.MatrixToTableFunction
 import is.hail.rvd.{RVD, RVDType}
@@ -27,9 +29,9 @@ case class PCA(entryField: String, k: Int, computeLoadings: Boolean)
       ),
     )
 
-  def preservesPartitionCounts: Boolean = false
+  override def preservesPartitionCounts: Boolean = false
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
     if (k < 1)
       fatal(s"""requested invalid number of components: $k
                |  Expect componenents >= 1""".stripMargin)
diff --git a/hail/hail/src/is/hail/methods/PCRelate.scala b/hail/hail/src/is/hail/methods/PCRelate.scala
index 32d1f1a88a1..6dcf0653436 100644
--- a/hail/hail/src/is/hail/methods/PCRelate.scala
+++ b/hail/hail/src/is/hail/methods/PCRelate.scala
@@ -5,6 +5,7 @@ import is.hail.expr.ir.TableValue
 import is.hail.expr.ir.functions.BlockMatrixToTableFunction
 import is.hail.linalg.BlockMatrix
 import is.hail.linalg.BlockMatrix.ops._
+import is.hail.linalg.implicits._
 import is.hail.types.virtual._
 import is.hail.utils._
 
@@ -152,10 +153,10 @@ case class PCRelate(
 
   def storageLevel: StorageLevel = PCRelate.defaultStorageLevel
 
-  def typ(bmType: BlockMatrixType, auxType: Type): TableType =
+  override def typ(bmType: BlockMatrixType, auxType: Type): TableType =
     TableType(sig, keys, TStruct.empty)
 
-  def execute(ctx: ExecuteContext, g: M, value: Any): TableValue = {
+  override def execute(ctx: ExecuteContext, g: M, value: Any): TableValue = {
     val pcs = rowsToBDM(value.asInstanceOf[IndexedSeq[IndexedSeq[java.lang.Double]]])
     assert(pcs.rows == g.nCols)
     val r = computeResult(ctx, g, pcs)
diff --git a/hail/hail/src/is/hail/methods/PoissonRegression.scala b/hail/hail/src/is/hail/methods/PoissonRegression.scala
index 02ba7579277..9805992c30d 100644
--- a/hail/hail/src/is/hail/methods/PoissonRegression.scala
+++ b/hail/hail/src/is/hail/methods/PoissonRegression.scala
@@ -2,7 +2,8 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
-import is.hail.expr.ir.{IntArrayBuilder, MatrixValue, TableValue}
+import is.hail.collection.IntArrayBuilder
+import is.hail.expr.ir.{MatrixValue, TableValue}
 import is.hail.expr.ir.functions.MatrixToTableFunction
 import is.hail.stats._
 import is.hail.types.virtual.{MatrixType, TFloat64, TStruct, TableType}
@@ -30,9 +31,9 @@ case class PoissonRegression(
     )
   }
 
-  def preservesPartitionCounts: Boolean = true
+  override def preservesPartitionCounts: Boolean = true
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
     val poisRegTest = PoissonRegressionTest.tests(test)
     val tableType = typ(mv.typ)
     val newRVDType = tableType.canonicalRVDType
diff --git a/hail/hail/src/is/hail/methods/Skat.scala b/hail/hail/src/is/hail/methods/Skat.scala
index 68381421020..cd682a06460 100644
--- a/hail/hail/src/is/hail/methods/Skat.scala
+++ b/hail/hail/src/is/hail/methods/Skat.scala
@@ -2,8 +2,10 @@ package is.hail.methods
 
 import is.hail.annotations.{Annotation, Region, UnsafeRow}
 import is.hail.backend.ExecuteContext
-import is.hail.expr.ir.{IntArrayBuilder, MatrixValue, TableValue}
+import is.hail.collection.{FastSeq, IntArrayBuilder}
+import is.hail.expr.ir.{MatrixValue, TableValue}
 import is.hail.expr.ir.functions.MatrixToTableFunction
+import is.hail.linalg.implicits._
 import is.hail.stats.{
   eigSymD, GeneralizedChiSquaredDistribution, LogisticRegressionModel, RegressionUtils,
 }
@@ -168,9 +170,9 @@ case class Skat(
     TableType(skatSchema, FastSeq("id"), TStruct.empty)
   }
 
-  def preservesPartitionCounts: Boolean = false
+  override def preservesPartitionCounts: Boolean = false
 
-  def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
+  override def execute(ctx: ExecuteContext, mv: MatrixValue): TableValue = {
 
     if (maxSize <= 0 || maxSize > 46340)
       fatal(s"Maximum group size must be in [1, 46340], got $maxSize")
diff --git a/hail/hail/src/is/hail/methods/VEP.scala b/hail/hail/src/is/hail/methods/VEP.scala
index da93581702e..0aa7f9d8faf 100644
--- a/hail/hail/src/is/hail/methods/VEP.scala
+++ b/hail/hail/src/is/hail/methods/VEP.scala
@@ -2,6 +2,9 @@ package is.hail.methods
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterator
 import is.hail.expr._
 import is.hail.expr.ir.TableValue
 import is.hail.expr.ir.functions.{RelationalFunctions, TableToTableFunction}
@@ -11,7 +14,6 @@ import is.hail.sparkextras.ContextRDD
 import is.hail.types.physical.PType
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 import is.hail.variant.{Locus, RegionValueVariant}
 import is.hail.variant.VariantMethods.locusAllelesToString
 
@@ -20,7 +22,7 @@ import scala.jdk.CollectionConverters._
 
 import com.fasterxml.jackson.core.JsonParseException
 import org.apache.spark.sql.Row
-import org.json4s.{Formats, JValue}
+import org.json4s.{DefaultFormats, Formats, JValue}
 import org.json4s.jackson.JsonMethods
 
 case class VEPConfiguration(
@@ -33,7 +35,7 @@ object VEP {
 
   def readConfiguration(fs: FS, path: String): VEPConfiguration = {
     val jv = using(fs.open(path))(in => JsonMethods.parse(in))
-    implicit val formats: Formats = defaultJSONFormats + new TStructSerializer
+    implicit val formats: Formats = DefaultFormats + new TStructSerializer
     jv.extract[VEPConfiguration]
   }
 
diff --git a/hail/hail/src/is/hail/package.scala b/hail/hail/src/is/hail/package.scala
deleted file mode 100644
index bda02673f3c..00000000000
--- a/hail/hail/src/is/hail/package.scala
+++ /dev/null
@@ -1,73 +0,0 @@
-package is
-
-import java.io.InputStream
-
-package object hail {
-
-  private object HailBuildInfo {
-
-    import is.hail.utils._
-
-    import java.util.Properties
-
-    val (
-      hail_revision: String,
-      hail_spark_version: String,
-      hail_pip_version: String,
-      hail_build_configuration: BuildConfiguration,
-    ) =
-      loadFromResource[(String, String, String, BuildConfiguration)]("build-info.properties") {
-        (is: InputStream) =>
-          val unknownProp = "<unknown>"
-          val props = new Properties()
-          props.load(is)
-          (
-            props.getProperty("revision", unknownProp),
-            props.getProperty("sparkVersion", unknownProp),
-            props.getProperty("hailPipVersion", unknownProp), {
-              val c = props.getProperty("hailBuildConfiguration", "debug")
-              BuildConfiguration.parseString(c).getOrElse(
-                throw new IllegalArgumentException(
-                  s"Illegal 'hailBuildConfiguration' entry in 'build-info.properties': '$c'."
-                )
-              )
-            },
-          )
-      }
-  }
-
-  val HAIL_REVISION = HailBuildInfo.hail_revision
-  val HAIL_SPARK_VERSION = HailBuildInfo.hail_spark_version
-  val HAIL_PIP_VERSION = HailBuildInfo.hail_pip_version
-
-  // FIXME: probably should use tags or something to choose English name
-  val HAIL_PRETTY_VERSION = HAIL_PIP_VERSION + "-" + HAIL_REVISION.substring(0, 12)
-
-  val HAIL_BUILD_CONFIGURATION = HailBuildInfo.hail_build_configuration
-}
-
-sealed trait BuildConfiguration extends Product with Serializable {
-  def isDebug: Boolean
-}
-
-object BuildConfiguration {
-  case object Release extends BuildConfiguration {
-    override def isDebug: Boolean = false
-  }
-
-  case object Debug extends BuildConfiguration {
-    override def isDebug: Boolean = true
-  }
-
-  case object CI extends BuildConfiguration {
-    override def isDebug: Boolean = true
-  }
-
-  def parseString(c: String): Option[BuildConfiguration] =
-    c match {
-      case "release" => Some(BuildConfiguration.Release)
-      case "dev" => Some(BuildConfiguration.Debug)
-      case "ci" => Some(BuildConfiguration.CI)
-      case _ => None
-    }
-}
diff --git a/hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala b/hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala
index 17b0cedad3d..035ecb7449f 100644
--- a/hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala
+++ b/hail/hail/src/is/hail/rvd/AbstractRVDSpec.scala
@@ -2,10 +2,12 @@ package is.hail.rvd
 
 import is.hail.annotations._
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.compatibility
 import is.hail.expr.{ir, JSONAnnotationImpex}
 import is.hail.expr.ir.{
-  flatMapIR, IR, PartitionNativeReader, PartitionZippedIndexedNativeReader,
+  flatMapIR, partFile, IR, PartitionNativeReader, PartitionZippedIndexedNativeReader,
   PartitionZippedNativeReader,
 }
 import is.hail.expr.ir.defs.{Literal, ReadPartition, Ref, ToStream}
@@ -13,11 +15,11 @@ import is.hail.expr.ir.lowering.{TableStage, TableStageDependency}
 import is.hail.io._
 import is.hail.io.fs.FS
 import is.hail.io.index.{InternalNodeBuilder, LeafNodeBuilder}
+import is.hail.sparkextras.implicits.RichContextRDDRegionValue
 import is.hail.types.encoded.ETypeSerializer
 import is.hail.types.physical._
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 
@@ -308,15 +310,15 @@ case class IndexSpec2(
   _annotationType: Type,
   _offsetField: Option[String] = None,
 ) extends AbstractIndexSpec {
-  def relPath: String = _relPath
+  override def relPath: String = _relPath
 
-  def leafCodec: AbstractTypedCodecSpec = _leafCodec
+  override def leafCodec: AbstractTypedCodecSpec = _leafCodec
 
-  def internalNodeCodec: AbstractTypedCodecSpec = _internalNodeCodec
+  override def internalNodeCodec: AbstractTypedCodecSpec = _internalNodeCodec
 
-  def keyType: Type = _keyType
+  override def keyType: Type = _keyType
 
-  def annotationType: Type = _annotationType
+  override def annotationType: Type = _annotationType
 
   override def offsetField: Option[String] = _offsetField
 }
@@ -462,11 +464,11 @@ case class IndexedRVDSpec2(
 
   require(codecSpec2.encodedType.required)
 
-  def typedCodecSpec: AbstractTypedCodecSpec = codecSpec2
+  override def typedCodecSpec: AbstractTypedCodecSpec = codecSpec2
 
-  def indexSpec: AbstractIndexSpec = _indexSpec
+  override def indexSpec: AbstractIndexSpec = _indexSpec
 
-  def partitioner(sm: HailStateManager): RVDPartitioner = {
+  override def partitioner(sm: HailStateManager): RVDPartitioner = {
     val keyType = codecSpec2.encodedVirtualType.asInstanceOf[TStruct].select(key)._1
     val rangeBoundsType = TArray(TInterval(keyType))
     new RVDPartitioner(
@@ -480,9 +482,9 @@ case class IndexedRVDSpec2(
     )
   }
 
-  def partFiles: IndexedSeq[String] = _partFiles
+  override def partFiles: IndexedSeq[String] = _partFiles
 
-  def key: IndexedSeq[String] = _key
+  override def key: IndexedSeq[String] = _key
 
   val attrs: Map[String, String] = _attrs
 
@@ -597,7 +599,7 @@ case class OrderedRVDSpec2(
 
   require(codecSpec2.encodedType.required)
 
-  def partitioner(sm: HailStateManager): RVDPartitioner = {
+  override def partitioner(sm: HailStateManager): RVDPartitioner = {
     val keyType = codecSpec2.encodedVirtualType.asInstanceOf[TStruct].select(key)._1
     val rangeBoundsType = TArray(TInterval(keyType))
     new RVDPartitioner(
@@ -611,11 +613,11 @@ case class OrderedRVDSpec2(
     )
   }
 
-  def partFiles: IndexedSeq[String] = _partFiles
+  override def partFiles: IndexedSeq[String] = _partFiles
 
-  def key: IndexedSeq[String] = _key
+  override def key: IndexedSeq[String] = _key
 
-  def attrs: Map[String, String] = _attrs
+  override def attrs: Map[String, String] = _attrs
 
-  def typedCodecSpec: AbstractTypedCodecSpec = codecSpec2
+  override def typedCodecSpec: AbstractTypedCodecSpec = codecSpec2
 }
diff --git a/hail/hail/src/is/hail/rvd/KeyedRVD.scala b/hail/hail/src/is/hail/rvd/KeyedRVD.scala
index 51c916c83cf..94fa467a2c4 100644
--- a/hail/hail/src/is/hail/rvd/KeyedRVD.scala
+++ b/hail/hail/src/is/hail/rvd/KeyedRVD.scala
@@ -2,11 +2,11 @@ package is.hail.rvd
 
 import is.hail.annotations._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.mutable.Growable
 import is.hail.sparkextras._
 import is.hail.types.physical.PStruct
 import is.hail.types.virtual.TInterval
 import is.hail.utils._
-import is.hail.utils.compat.mutable.Growable
 
 class KeyedRVD(val rvd: RVD, val key: Int) {
   require(key <= rvd.typ.key.length && key >= 0)
diff --git a/hail/hail/src/is/hail/rvd/RVD.scala b/hail/hail/src/is/hail/rvd/RVD.scala
index f7acbb04ddd..10aaa68315d 100644
--- a/hail/hail/src/is/hail/rvd/RVD.scala
+++ b/hail/hail/src/is/hail/rvd/RVD.scala
@@ -4,17 +4,21 @@ import is.hail.annotations._
 import is.hail.asm4s.{theHailClassLoaderForSparkWorkers, HailClassLoader}
 import is.hail.backend.{ExecuteContext, HailStateManager, HailTaskContext}
 import is.hail.backend.spark.{SparkBackend, SparkTaskContext}
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{arrayToRichIndexedSeq, toRichIterable, toRichOrderedArray}
 import is.hail.expr.ir.InferPType
 import is.hail.expr.ir.PruneDeadFields.isSupertype
 import is.hail.expr.ir.agg.AggExecuteContextExtensions
 import is.hail.io._
 import is.hail.io.index.IndexWriter
+import is.hail.rvd.RVD.RichIteratorLong
 import is.hail.sparkextras._
+import is.hail.sparkextras.implicits._
 import is.hail.types.physical.{PCanonicalStruct, PInt64, PStruct}
 import is.hail.types.virtual.{MatrixType, TInterval, TStruct}
 import is.hail.utils._
 import is.hail.utils.PartitionCounts.{getPCSubsetOffset, incrementalPCSubsetOffset, PCSubsetOffset}
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.parallel.CollectionConverters._
 import scala.reflect.ClassTag
@@ -186,9 +190,9 @@ class RVD(
         new Iterator[Long] {
           var first = true
 
-          def hasNext: Boolean = it.hasNext
+          override def hasNext: Boolean = it.hasNext
 
-          def next(): Long = {
+          override def next(): Long = {
             val ptr = it.next()
 
             if (first)
@@ -1016,9 +1020,9 @@ class RVD(
     val sorted: RDD[((Int, Interval), Array[Byte])] = new ShuffledRDD(
       partitionKeyedIntervals,
       new Partitioner {
-        def getPartition(key: Any): Int = key.asInstanceOf[(Int, Interval)]._1
+        override def getPartition(key: Any): Int = key.asInstanceOf[(Int, Interval)]._1
 
-        def numPartitions: Int = nParts
+        override def numPartitions: Int = nParts
       },
     ).setKeyOrdering(Ordering.by[(Int, Interval), Interval](_._2)(intervalOrd))
 
@@ -1188,7 +1192,7 @@ object RVD extends Logging {
     type CRDD = ContextRDD[Long]
 
     val unkeyedCoercer: RVDCoercer = new RVDCoercer(fullType) {
-      def _coerce(typ: RVDType, crdd: CRDD): RVD = {
+      override def _coerce(typ: RVDType, crdd: CRDD): RVD = {
         assert(typ.key.isEmpty)
         unkeyed(typ.rowType, crdd)
       }
@@ -1198,7 +1202,7 @@ object RVD extends Logging {
       return unkeyedCoercer
 
     val emptyCoercer: RVDCoercer = new RVDCoercer(fullType) {
-      def _coerce(typ: RVDType, crdd: CRDD): RVD = empty(execCtx, typ)
+      override def _coerce(typ: RVDType, crdd: CRDD): RVD = empty(execCtx, typ)
     }
 
     val keyInfo = getKeyInfo(execCtx, fullType, partitionKey, keys)
@@ -1243,7 +1247,7 @@ object RVD extends Logging {
           bounds,
         )
 
-        def _coerce(typ: RVDType, crdd: CRDD): RVD =
+        override def _coerce(typ: RVDType, crdd: CRDD): RVD =
           RVD(typ, unfixedPartitioner, orderPartitions(crdd))
             .repartition(execCtx, newPartitioner, shuffle = false)
       }
@@ -1273,7 +1277,7 @@ object RVD extends Logging {
           pkBounds,
         )
 
-        def _coerce(typ: RVDType, crdd: CRDD): RVD = {
+        override def _coerce(typ: RVDType, crdd: CRDD): RVD = {
           RVD(
             typ.copy(key = typ.key.take(partitionKey)),
             unfixedPartitioner,
@@ -1292,7 +1296,7 @@ object RVD extends Logging {
         val newPartitioner =
           calculateKeyRanges(execCtx, this.fullType, keyInfo, keys.getNumPartitions, partitionKey)
 
-        def _coerce(typ: RVDType, crdd: CRDD): RVD =
+        override def _coerce(typ: RVDType, crdd: CRDD): RVD =
           RVD.unkeyed(typ.rowType, crdd)
             .repartition(execCtx, newPartitioner, shuffle = true, filter = false)
       }
@@ -1470,6 +1474,13 @@ object RVD extends Logging {
 
     fileData
   }
+
+  implicit class RichIteratorLong(private val it: Iterator[Long]) extends AnyVal {
+    def toIteratorRV(region: Region): Iterator[RegionValue] = {
+      val rv = RegionValue(region)
+      it.map { ptr => rv.setOffset(ptr); rv }
+    }
+  }
 }
 
 class BroadcastRVD(backend: SparkBackend, rvd: RVD) extends Serializable {
diff --git a/hail/hail/src/is/hail/rvd/RVDContext.scala b/hail/hail/src/is/hail/rvd/RVDContext.scala
index a8b2faf10ec..d4ec9c9f5f8 100644
--- a/hail/hail/src/is/hail/rvd/RVDContext.scala
+++ b/hail/hail/src/is/hail/rvd/RVDContext.scala
@@ -43,7 +43,7 @@ class RVDContext(val partitionRegion: Region, val r: Region) extends AutoCloseab
   def rvb = theRvb
 
   // frees the memory associated with this context
-  def close(): Unit = {
+  override def close(): Unit = {
     var e: Exception = null
     children.foreach { child =>
       try
diff --git a/hail/hail/src/is/hail/rvd/RVDPartitioner.scala b/hail/hail/src/is/hail/rvd/RVDPartitioner.scala
index c4adeaa36c0..dabe8eddf85 100644
--- a/hail/hail/src/is/hail/rvd/RVDPartitioner.scala
+++ b/hail/hail/src/is/hail/rvd/RVDPartitioner.scala
@@ -2,10 +2,13 @@ package is.hail.rvd
 
 import is.hail.annotations._
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{arrayToRichIndexedSeq, toRichIterable}
 import is.hail.expr.ir.defs.Literal
+import is.hail.sparkextras.implicits._
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import org.apache.commons.lang3.builder.HashCodeBuilder
 import org.apache.spark.{Partitioner, SparkContext}
@@ -114,9 +117,9 @@ class RVDPartitioner(
     val selfBc = broadcast(sc)
 
     new Partitioner {
-      def numPartitions: Int = selfBc.value.numPartitions
+      override def numPartitions: Int = selfBc.value.numPartitions
 
-      def getPartition(key: Any): Int = selfBc.value.lowerBound(key)
+      override def getPartition(key: Any): Int = selfBc.value.lowerBound(key)
     }
   }
 
diff --git a/hail/hail/src/is/hail/rvd/RVDType.scala b/hail/hail/src/is/hail/rvd/RVDType.scala
index d940af030bf..05f2e700084 100644
--- a/hail/hail/src/is/hail/rvd/RVDType.scala
+++ b/hail/hail/src/is/hail/rvd/RVDType.scala
@@ -2,6 +2,7 @@ package is.hail.rvd
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.IRParser
 import is.hail.types.physical.{PInterval, PStruct}
 import is.hail.utils._
@@ -96,7 +97,7 @@ final case class RVDType(rowType: PStruct, key: IndexedSeq[String]) extends Seri
       // Left is a point, right is an interval.
       // Returns -1 if point is below interval, 0 if it is inside, and 1 if it
       // is above, always considering missing greatest.
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
 
         val leftDefined = t1.isFieldDefined(o1, f1)
         val rightDefined = t2.isFieldDefined(o2, f2)
@@ -128,10 +129,10 @@ final case class RVDType(rowType: PStruct, key: IndexedSeq[String]) extends Seri
     val wrv = WritableRegionValue(sm, kType, region)
     val kRowOrdering = kRowOrd(sm)
 
-    def setFiniteValue(representative: RegionValue): Unit =
+    override def setFiniteValue(representative: RegionValue): Unit =
       wrv.setSelect(rowType, kFieldIdx, representative)
 
-    def compareFinite(rv: RegionValue): Int =
+    override def compareFinite(rv: RegionValue): Int =
       kRowOrdering.compare(wrv.value, rv)
   }
 
@@ -188,7 +189,7 @@ object RVDType {
     val nFields = fields1.length
 
     new UnsafeOrdering {
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
         var i = 0
         var hasMissing = false
         while (i < nFields) {
diff --git a/hail/hail/src/is/hail/services/BatchClient.scala b/hail/hail/src/is/hail/services/BatchClient.scala
index 2404efe1915..0e6ae69c838 100644
--- a/hail/hail/src/is/hail/services/BatchClient.scala
+++ b/hail/hail/src/is/hail/services/BatchClient.scala
@@ -1,6 +1,6 @@
 package is.hail.services
 
-import is.hail.expr.ir.ByteArrayBuilder
+import is.hail.collection.{ByteArrayBuilder, FastSeq}
 import is.hail.services.BatchClient.{
   BunchMaxSizeBytes, JarSpecSerializer, JobGroupResponseDeserializer, JobGroupStateDeserializer,
   JobListEntryDeserializer, JobProcessRequestSerializer, JobStateDeserializer,
diff --git a/hail/hail/src/is/hail/services/JSONLogLayout.scala b/hail/hail/src/is/hail/services/JSONLogLayout.scala
deleted file mode 100644
index c9984eec19d..00000000000
--- a/hail/hail/src/is/hail/services/JSONLogLayout.scala
+++ /dev/null
@@ -1,85 +0,0 @@
-package is.hail.services
-
-import is.hail.utils.compat.immutable.ArraySeq
-
-import java.io.StringWriter
-import java.text._
-import java.util.function._
-
-import org.apache.log4j._
-import org.apache.log4j.spi._
-import org.json4s._
-import org.json4s.jackson.JsonMethods
-
-class DateFormatter {
-  private[this] val fmt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS")
-  private[this] val buffer = new StringBuffer()
-  private[this] val fp = new FieldPosition(0)
-
-  def format(milliseconds: Long): String = {
-    buffer.setLength(0)
-    fmt.format(milliseconds, buffer, fp)
-    buffer.toString
-  }
-}
-
-object JSONLogLayout {
-  private val datefmt = ThreadLocal.withInitial(new Supplier[DateFormatter]() {
-    def get() = new DateFormatter()
-  })
-}
-
-class JSONLogLayout extends Layout {
-  import JSONLogLayout._
-
-  def ignoresThrowable(): Boolean = false
-
-  def activateOptions(): Unit = ()
-
-  def format(event: LoggingEvent): String = {
-    val threadName = event.getThreadName();
-    val timestamp = event.getTimeStamp();
-    val mdc = event.getProperties();
-    val ndc = event.getNDC();
-    val throwableInfo = event.getThrowableInformation()
-    val locationInfo = event.getLocationInformation()
-    val fields = ArraySeq.newBuilder[JField]
-    fields += JField("@version", JInt(1))
-    fields += JField("@timestamp", JString(datefmt.get.format(timestamp)))
-    fields += JField("message", JString(event.getRenderedMessage()))
-    fields += JField("filename", JString(locationInfo.getFileName()))
-    fields += JField("line_number", JString(locationInfo.getLineNumber()))
-    fields += JField("class", JString(locationInfo.getClassName()))
-    fields += JField("method", JString(locationInfo.getMethodName()))
-    fields += JField("logger_name", JString(event.getLoggerName()))
-
-    val mdcFields = ArraySeq.newBuilder[JField]
-    mdc.forEach(new BiConsumer[Any, Any]() {
-      def accept(key: Any, value: Any): Unit =
-        mdcFields += JField(key.toString, JString(value.toString))
-    })
-    fields += JField("mdc", JObject(mdcFields.result(): _*))
-
-    fields += JField("ndc", JString(ndc))
-    fields += JField("severity", JString(event.getLevel().toString()))
-    fields += JField("thread_name", JString(threadName))
-
-    if (throwableInfo != null) {
-      fields += JField(
-        "exception_class",
-        JString(throwableInfo.getThrowable().getClass().getCanonicalName()),
-      )
-      fields += JField("exception_message", JString(throwableInfo.getThrowable().getMessage()))
-      fields += JField(
-        "exception_stacktrace",
-        JString(formatException(throwableInfo.getThrowable())),
-      )
-    }
-    val jsonEvent = JObject(fields.result(): _*)
-
-    val sw = new StringWriter()
-    JsonMethods.mapper.writeValue(sw, jsonEvent)
-    sw.append('\n')
-    sw.toString()
-  }
-}
diff --git a/hail/hail/src/is/hail/sparkextras/BlockedRDD.scala b/hail/hail/src/is/hail/sparkextras/BlockedRDD.scala
index 9006acbe901..95830b8337e 100644
--- a/hail/hail/src/is/hail/sparkextras/BlockedRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/BlockedRDD.scala
@@ -1,7 +1,9 @@
 package is.hail.sparkextras
 
-import is.hail.utils._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 
+import scala.collection.compat._
 import scala.reflect.ClassTag
 
 import org.apache.spark.{Dependency, NarrowDependency, Partition, TaskContext}
@@ -38,7 +40,7 @@ class BlockedRDD[T](
 
   override def getDependencies: Seq[Dependency[_]] =
     FastSeq(new NarrowDependency(prev) {
-      def getParents(id: Int): Seq[Int] =
+      override def getParents(id: Int): Seq[Int] =
         partitions(id).asInstanceOf[BlockedRDDPartition].range
     })
 
@@ -54,15 +56,12 @@ class BlockedRDD[T](
     val locationAvail = range.flatMap(i =>
       prev.preferredLocations(prevPartitions(i))
     )
-      .groupBy(identity)
-      .mapValues(_.length)
+      .counter()
 
     if (locationAvail.isEmpty)
       return FastSeq.empty[String]
 
     val m = locationAvail.values.max
-    locationAvail.filter(_._2 == m)
-      .keys
-      .toFastSeq
+    locationAvail.filter(_._2 == m).keys.toFastSeq
   }
 }
diff --git a/hail/hail/src/is/hail/sparkextras/ContextPairRDDFunctions.scala b/hail/hail/src/is/hail/sparkextras/ContextPairRDDFunctions.scala
deleted file mode 100644
index 34e7f54ef98..00000000000
--- a/hail/hail/src/is/hail/sparkextras/ContextPairRDDFunctions.scala
+++ /dev/null
@@ -1,19 +0,0 @@
-package is.hail.sparkextras
-
-import scala.reflect.ClassTag
-
-import org.apache.spark._
-import org.apache.spark.rdd._
-
-class ContextPairRDDFunctions[K: ClassTag, V: ClassTag](
-  crdd: ContextRDD[(K, V)]
-) {
-  // FIXME: this needs to take RDDs with values that are not in region-value-land.
-  def partitionBy(p: Partitioner): ContextRDD[(K, V)] =
-    if (crdd.partitioner.contains(p)) crdd
-    else ContextRDD.weaken(
-      new ShuffledRDD[K, V, V](crdd.run, p)
-    )
-
-  def values: ContextRDD[V] = crdd.map(_._2)
-}
diff --git a/hail/hail/src/is/hail/sparkextras/ContextRDD.scala b/hail/hail/src/is/hail/sparkextras/ContextRDD.scala
index 0084d094b45..e5557f23331 100644
--- a/hail/hail/src/is/hail/sparkextras/ContextRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/ContextRDD.scala
@@ -3,6 +3,7 @@ package is.hail.sparkextras
 import is.hail.backend.ExecuteContext
 import is.hail.backend.spark.{SparkBackend, SparkTaskContext}
 import is.hail.rvd.RVDContext
+import is.hail.sparkextras.implicits.{toRichContextRDD, toRichRDD, toRichSC}
 import is.hail.utils._
 
 import scala.collection.compat._
@@ -31,9 +32,9 @@ abstract class Combiner[U] {
 class CommutativeAndAssociativeCombiner[U](zero: => U, combine: (U, U) => U) extends Combiner[U] {
   var state: U = zero
 
-  def combine(i: Int, value0: U): Unit = state = combine(state, value0)
+  override def combine(i: Int, value0: U): Unit = state = combine(state, value0)
 
-  def result(): U = state
+  override def result(): U = state
 }
 
 class AssociativeCombiner[U](zero: => U, combine: (U, U) => U) extends Combiner[U] with Logging {
@@ -44,7 +45,7 @@ class AssociativeCombiner[U](zero: => U, combine: (U, U) => U) extends Combiner[
   // U it holds.
   private val t = new java.util.TreeMap[Int, TreeValue]()
 
-  def combine(i: Int, value0: U): Unit = {
+  override def combine(i: Int, value0: U): Unit = {
     logger.info(s"at result $i, AssociativeCombiner contains ${t.size()} queued results")
     var value = value0
     var end = i
@@ -69,7 +70,7 @@ class AssociativeCombiner[U](zero: => U, combine: (U, U) => U) extends Combiner[
     t.put(i, TreeValue(value, end))
   }
 
-  def result(): U = {
+  override def result(): U = {
     // after 'result' returns, 't' owns no values.
     val n = t.size()
     if (n > 0) {
@@ -295,13 +296,13 @@ class ContextRDD[T: ClassTag](
     f: (RVDContext, T, U) => V
   ): ContextRDD[V] = czipPartitions(that, preservesPartitioning) { (ctx, l, r) =>
     new Iterator[V] {
-      def hasNext = {
+      override def hasNext = {
         val lhn = l.hasNext
         val rhn = r.hasNext
         assert(lhn == rhn)
         lhn
       }
-      def next(): V =
+      override def next(): V =
         f(ctx, l.next(), r.next())
     }
   }
@@ -420,7 +421,7 @@ class ContextRDD[T: ClassTag](
 }
 
 private class CRDDCoalescer(partEnds: Array[Int]) extends PartitionCoalescer with Serializable {
-  def coalesce(maxPartitions: Int, prev: RDD[_]): Array[PartitionGroup] = {
+  override def coalesce(maxPartitions: Int, prev: RDD[_]): Array[PartitionGroup] = {
     assert(maxPartitions == partEnds.length)
     val groups = Array.fill(maxPartitions)(new PartitionGroup())
     val parts = prev.partitions
diff --git a/hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala b/hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala
index 94e00942a2f..bedb3f97ba3 100644
--- a/hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/IndexReadRDD.scala
@@ -16,7 +16,7 @@ class IndexReadRDD[T: ClassTag](
   @transient val intervalBounds: Option[Array[Interval]],
   f: (IndexedFilePartition, TaskContext) => T,
 ) extends RDD[T](SparkBackend.sparkContext, Nil) {
-  def getPartitions: Array[Partition] =
+  override def getPartitions: Array[Partition] =
     Array.tabulate(partFiles.length) { i =>
       IndexedFilePartition(i, partFiles(i), intervalBounds.map(_(i)))
     }
diff --git a/hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala b/hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
index 8b04d55d2e4..8c80c9ad76c 100644
--- a/hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/MapPartitionsWithValueRDD.scala
@@ -10,7 +10,7 @@ case class MapPartitionsWithValueRDDPartition[V](
   parentPartition: Partition,
   value: V,
 ) extends Partition {
-  def index: Int = parentPartition.index
+  override def index: Int = parentPartition.index
 }
 
 class MapPartitionsWithValueRDD[T: ClassTag, U: ClassTag, V](
diff --git a/hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala b/hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala
index fd7d59735df..f2e95f33a8e 100644
--- a/hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/OriginUnionRDD.scala
@@ -1,6 +1,6 @@
 package is.hail.sparkextras
 
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.collection.compat.immutable.ArraySeq
 
 import scala.reflect.ClassTag
 
diff --git a/hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala b/hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala
index f8b5225c991..10d208b6b74 100644
--- a/hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/ReorderedPartitionsRDD.scala
@@ -1,6 +1,6 @@
 package is.hail.sparkextras
 
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import scala.reflect.ClassTag
 
diff --git a/hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala b/hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
index cfd1054d297..30c3389469d 100644
--- a/hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
+++ b/hail/hail/src/is/hail/sparkextras/RepartitionedOrderedRDD2.scala
@@ -2,6 +2,7 @@ package is.hail.sparkextras
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.rvd.{PartitionBoundOrdering, RVD, RVDContext, RVDPartitioner, RVDType}
 import is.hail.utils._
 
@@ -46,7 +47,7 @@ class RepartitionedOrderedRDD2 private (
   val typ: RVDType = prev.typ
   val kOrd: ExtendedOrdering = PartitionBoundOrdering(sm, typ.kType.virtualType)
 
-  def getPartitions: Array[Partition] = {
+  override def getPartitions: Array[Partition] = {
     require(newRangeBounds.forall { i =>
       typ.kType.virtualType.relaxedTypeCheck(i.start) && typ.kType.virtualType.relaxedTypeCheck(
         i.end
@@ -109,7 +110,7 @@ class RepartitionedOrderedRDD2 private (
           innerRegion.clear()
         }
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (pulled)
             return true
 
@@ -126,7 +127,7 @@ class RepartitionedOrderedRDD2 private (
           true
         }
 
-        def next(): Long = {
+        override def next(): Long = {
           // hasNext() must be called before next() to fill `current`
           if (!hasNext)
             throw new NoSuchElementException
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichContextRDD.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDD.scala
similarity index 91%
rename from hail/hail/src/is/hail/utils/richUtils/RichContextRDD.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichContextRDD.scala
index ecfae69f4c6..ae7e6e48701 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichContextRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDD.scala
@@ -1,13 +1,14 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import is.hail.annotations.RegionPool
 import is.hail.backend.ExecuteContext
+import is.hail.expr.ir.partFile
 import is.hail.io.FileWriteMetadata
 import is.hail.io.fs.FS
 import is.hail.io.index.IndexWriter
 import is.hail.rvd.RVDContext
 import is.hail.sparkextras._
-import is.hail.utils._
+import is.hail.utils.digitsNeeded
 
 import scala.reflect.ClassTag
 
@@ -61,15 +62,15 @@ object RichContextRDD {
   }
 }
 
-class RichContextRDD[T: ClassTag](crdd: ContextRDD[T]) {
+class RichContextRDD[T](val crdd: ContextRDD[T]) extends AnyVal {
 
-  def cleanupRegions: ContextRDD[T] = {
+  def cleanupRegions(implicit CT: ClassTag[T]): ContextRDD[T] = {
     crdd.cmapPartitionsAndContext { (ctx, part) =>
       val it = part.flatMap(_(ctx))
       new Iterator[T]() {
         private[this] var cleared: Boolean = false
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (!cleared) {
             cleared = true
             ctx.region.clear()
@@ -77,7 +78,7 @@ class RichContextRDD[T: ClassTag](crdd: ContextRDD[T]) {
           it.hasNext
         }
 
-        def next(): T = {
+        override def next(): T = {
           if (!cleared) {
             ctx.region.clear()
           }
diff --git a/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDPair.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDPair.scala
new file mode 100644
index 00000000000..26b3fcf55c2
--- /dev/null
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDPair.scala
@@ -0,0 +1,18 @@
+package is.hail.sparkextras.implicits
+
+import is.hail.sparkextras.ContextRDD
+
+import scala.reflect.ClassTag
+
+import org.apache.spark._
+import org.apache.spark.rdd._
+
+class RichContextRDDPair[K, V](val crdd: ContextRDD[(K, V)]) extends AnyVal {
+  // FIXME: this needs to take RDDs with values that are not in region-value-land.
+  def partitionBy(p: Partitioner)(implicit KT: ClassTag[K], VT: ClassTag[V]): ContextRDD[(K, V)] =
+    if (crdd.partitioner.contains(p)) crdd
+    else ContextRDD.weaken(new ShuffledRDD[K, V, V](crdd.run, p))
+
+  def values(implicit VT: ClassTag[V]): ContextRDD[V] =
+    crdd.map(_._2)
+}
diff --git a/hail/hail/src/is/hail/io/RichContextRDDRegionValue.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRegionValue.scala
similarity index 95%
rename from hail/hail/src/is/hail/io/RichContextRDDRegionValue.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRegionValue.scala
index 07c5b1dde55..e239543a7b6 100644
--- a/hail/hail/src/is/hail/io/RichContextRDDRegionValue.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRegionValue.scala
@@ -1,16 +1,18 @@
-package is.hail.io
+package is.hail.sparkextras.implicits
 
 import is.hail.annotations._
 import is.hail.asm4s.{theHailClassLoaderForSparkWorkers, HailClassLoader}
 import is.hail.backend.ExecuteContext
 import is.hail.backend.spark.SparkTaskContext
+import is.hail.expr.ir.partFile
+import is.hail.io.{AbstractTypedCodecSpec, Encoder, FileWriteMetadata}
 import is.hail.io.fs.FS
 import is.hail.io.index.IndexWriter
-import is.hail.rvd.{AbstractIndexSpec, MakeRVDSpec, RVDContext, RVDPartitioner, RVDType}
+import is.hail.rvd._
 import is.hail.sparkextras._
 import is.hail.types.physical._
 import is.hail.utils._
-import is.hail.utils.richUtils.ByteTrackingOutputStream
+import is.hail.utils.implicits.ByteTrackingOutputStream
 
 import java.io._
 
@@ -204,7 +206,7 @@ class RichContextRDDLong(val crdd: ContextRDD[Long]) extends AnyVal {
       new Iterator[Long]() {
         private[this] var cleared: Boolean = false
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (!cleared) {
             cleared = true
             producerCtx.region.clear()
@@ -212,7 +214,7 @@ class RichContextRDDLong(val crdd: ContextRDD[Long]) extends AnyVal {
           it.hasNext
         }
 
-        def next(): Long = {
+        override def next(): Long = {
           if (!cleared) {
             producerCtx.region.clear()
           }
@@ -264,7 +266,7 @@ class RichContextRDDRegionValue(val crdd: ContextRDD[RegionValue]) extends AnyVa
       new Iterator[RegionValue]() {
         private[this] var cleared: Boolean = false
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (!cleared) {
             cleared = true
             producerCtx.region.clear()
@@ -272,7 +274,7 @@ class RichContextRDDRegionValue(val crdd: ContextRDD[RegionValue]) extends AnyVa
           it.hasNext
         }
 
-        def next(): RegionValue = {
+        override def next(): RegionValue = {
           if (!cleared) {
             producerCtx.region.clear()
           }
@@ -297,7 +299,7 @@ class RichContextRDDRegionValue(val crdd: ContextRDD[RegionValue]) extends AnyVa
       new Iterator[RegionValue]() {
         private[this] var cleared: Boolean = false
 
-        def hasNext: Boolean = {
+        override def hasNext: Boolean = {
           if (!cleared) {
             cleared = true
             ctx.region.clear()
@@ -305,7 +307,7 @@ class RichContextRDDRegionValue(val crdd: ContextRDD[RegionValue]) extends AnyVa
           it.hasNext
         }
 
-        def next(): RegionValue = {
+        override def next(): RegionValue = {
           if (!cleared) {
             ctx.region.clear()
           }
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichContextRDDRow.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRow.scala
similarity index 84%
rename from hail/hail/src/is/hail/utils/richUtils/RichContextRDDRow.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRow.scala
index c075eda9a20..ae4d06494f6 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichContextRDDRow.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichContextRDDRow.scala
@@ -1,8 +1,7 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import is.hail.sparkextras.ContextRDD
 import is.hail.types.physical.PStruct
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichJoinedRegionValue.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichJoinedRegionValue.scala
similarity index 89%
rename from hail/hail/src/is/hail/utils/richUtils/RichJoinedRegionValue.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichJoinedRegionValue.scala
index bd07f29b049..8f8bf3e7f0f 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichJoinedRegionValue.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichJoinedRegionValue.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import is.hail.annotations.{JoinedRegionValue, RegionValue}
 import is.hail.types.physical.PType
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichPairRDD.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichPairRDD.scala
similarity index 86%
rename from hail/hail/src/is/hail/utils/richUtils/RichPairRDD.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichPairRDD.scala
index 1f17fcdc3a7..f27d3be9a58 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichPairRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichPairRDD.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import org.apache.spark.rdd.RDD
 
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichRDD.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichRDD.scala
similarity index 91%
rename from hail/hail/src/is/hail/utils/richUtils/RichRDD.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichRDD.scala
index 74d01f4d4ae..6fec789da8b 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichRDD.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichRDD.scala
@@ -1,6 +1,9 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.{toRichIterable, toRichOrderedSeq}
+import is.hail.expr.ir.ExportType
 import is.hail.io.FileWriteMetadata
 import is.hail.io.compress.{BGzipCodec, ComposableBGzipCodec, ComposableBGzipOutputStream}
 import is.hail.sparkextras._
@@ -161,14 +164,14 @@ class RichRDD[T](val r: RDD[T]) extends AnyVal {
     new RDD[T](
       r.sparkContext,
       FastSeq(new NarrowDependency[T](r) {
-        def getParents(partitionId: Int): Seq[Int] = FastSeq(keep(partitionId))
+        override def getParents(partitionId: Int): Seq[Int] = FastSeq(keep(partitionId))
       }),
     ) {
-      def getPartitions: Array[Partition] = keep.indices.map { i =>
+      override def getPartitions: Array[Partition] = keep.indices.map { i =>
         SubsetRDDPartition(i, parentPartitions(keep(i)))
       }.toArray
 
-      def compute(split: Partition, context: TaskContext): Iterator[T] =
+      override def compute(split: Partition, context: TaskContext): Iterator[T] =
         r.compute(split.asInstanceOf[SubsetRDDPartition].parentPartition, context)
 
       @transient override val partitioner: Option[Partitioner] = newPartitioner
@@ -193,17 +196,17 @@ class RichRDD[T](val r: RDD[T]) extends AnyVal {
     new RDD[T](
       r.sparkContext,
       FastSeq(new NarrowDependency[T](r) {
-        def getParents(partitionId: Int): Seq[Int] = newToOldPI.get(partitionId) match {
+        override def getParents(partitionId: Int): Seq[Int] = newToOldPI.get(partitionId) match {
           case Some(oldPI) => Array(oldPI)
           case None => Array.empty[Int]
         }
       }),
     ) {
-      def getPartitions: Array[Partition] = Array.tabulate(newNPartitions) { i =>
+      override def getPartitions: Array[Partition] = Array.tabulate(newNPartitions) { i =>
         SupersetRDDPartition(i, newToOldPI.get(i).map(parentPartitions))
       }
 
-      def compute(split: Partition, context: TaskContext): Iterator[T] =
+      override def compute(split: Partition, context: TaskContext): Iterator[T] =
         split.asInstanceOf[SupersetRDDPartition].maybeParentPartition match {
           case Some(part) => r.compute(part, context)
           case None => newPIPartition(split.index)
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichRow.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichRow.scala
similarity index 72%
rename from hail/hail/src/is/hail/utils/richUtils/RichRow.scala
rename to hail/hail/src/is/hail/sparkextras/implicits/RichRow.scala
index 878505590de..c25276ad463 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichRow.scala
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichRow.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.sparkextras.implicits
 
 import org.apache.spark.sql.Row
 
@@ -21,6 +21,18 @@ class RichRow(r: Row) {
     require(newSize <= r.size)
     Row.fromSeq(Array.tabulate(newSize)(i => r.get(i)))
   }
+
+  def iterator: Iterator[Any] =
+    new Iterator[Any] {
+      private[this] var idx: Int = 0
+      override def hasNext: Boolean = idx < r.size
+
+      override def next(): Any = {
+        val a = r(idx)
+        idx += 1
+        a
+      }
+    }
 }
 
 class RowWithDeletedField(parent: Row, deleteIdx: Int) extends Row {
diff --git a/hail/hail/src/is/hail/sparkextras/implicits/RichRowIterator.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichRowIterator.scala
new file mode 100644
index 00000000000..f1c6e23b422
--- /dev/null
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichRowIterator.scala
@@ -0,0 +1,11 @@
+package is.hail.sparkextras.implicits
+
+import is.hail.annotations.Region
+import is.hail.types.physical.PStruct
+
+import org.apache.spark.sql.Row
+
+class RichRowIterator(val it: Iterator[Row]) extends AnyVal {
+  def copyToRegion(region: Region, rowTyp: PStruct): Iterator[Long] =
+    it.map(row => rowTyp.unstagedStoreJavaObject(null, row, region))
+}
diff --git a/hail/hail/src/is/hail/sparkextras/implicits/RichSparkContext.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichSparkContext.scala
new file mode 100644
index 00000000000..ca5afc13fd2
--- /dev/null
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichSparkContext.scala
@@ -0,0 +1,50 @@
+package is.hail.sparkextras.implicits
+
+import is.hail.utils._
+
+import org.apache.hadoop.mapred.FileSplit
+import org.apache.hadoop.mapreduce.lib.input.{FileSplit => NewFileSplit}
+import org.apache.spark.{Partition, SparkContext}
+import org.apache.spark.rdd.RDD
+
+class RichSparkContext(val sc: SparkContext) extends AnyVal {
+  def textFilesLines(files: Array[String], nPartitions: Int = sc.defaultMinPartitions)
+    : RDD[WithContext[String]] = {
+
+    /* Don't use:
+     * sc.union(files.map(sc.textFile, nPartitions)) since it asks for nPartitions per file instead
+     * of nPartitions over all. */
+    val rdd = sc.textFile(files.mkString(","), nPartitions)
+    val partitionFile = rdd.partitions.map(partitionPath)
+
+    rdd
+      .mapPartitionsWithIndex { case (i, it) =>
+        // FIXME subclass TextInputFormat to return (file, line)
+        val file = partitionFile(i)
+        it.map(line => WithContext(line, Context(line, file, None)))
+      }
+  }
+
+  /* Use reflection to get the path of a partition coming from a Parquet read. This requires
+   * accessing Spark internal interfaces. It works with Spark 1 and 2 and doesn't depend on the
+   * location of the Parquet package (parquet vs org.apache.parquet) which can vary between
+   * distributions. */
+  def partitionPath(p: Partition): String = {
+    p.getClass.getCanonicalName match {
+      case "org.apache.spark.rdd.SqlNewHadoopPartition" =>
+        val split = invokeMethod(invokeMethod(p, "serializableHadoopSplit"), "value").asInstanceOf[
+          NewFileSplit
+        ]
+        split.getPath.getName
+
+      case "org.apache.spark.sql.execution.datasources.FilePartition" =>
+        val files = invokeMethod(p, "files").asInstanceOf[Seq[_ <: AnyRef]]
+        assert(files.length == 1)
+        invokeMethod(files.head, "filePath").asInstanceOf[String]
+
+      case "org.apache.spark.rdd.HadoopPartition" =>
+        val split = invokeMethod(invokeMethod(p, "inputSplit"), "value").asInstanceOf[FileSplit]
+        split.getPath.getName
+    }
+  }
+}
diff --git a/hail/hail/src/is/hail/sparkextras/implicits/RichTaskContext.scala b/hail/hail/src/is/hail/sparkextras/implicits/RichTaskContext.scala
new file mode 100644
index 00000000000..8ba7cdce048
--- /dev/null
+++ b/hail/hail/src/is/hail/sparkextras/implicits/RichTaskContext.scala
@@ -0,0 +1,11 @@
+package is.hail.sparkextras.implicits
+
+import org.apache.spark.TaskContext
+
+class RichTaskContext(val ctx: TaskContext) extends AnyVal {
+  def partSuffix: String = {
+    val rng = new java.security.SecureRandom()
+    val fileUUID = new java.util.UUID(rng.nextLong(), rng.nextLong())
+    s"${ctx.stageId()}-${ctx.partitionId()}-${ctx.attemptNumber()}-$fileUUID"
+  }
+}
diff --git a/hail/hail/src/is/hail/sparkextras/implicits/package.scala b/hail/hail/src/is/hail/sparkextras/implicits/package.scala
new file mode 100644
index 00000000000..3f76e41018a
--- /dev/null
+++ b/hail/hail/src/is/hail/sparkextras/implicits/package.scala
@@ -0,0 +1,41 @@
+package is.hail.sparkextras
+
+import is.hail.annotations.{JoinedRegionValue, RegionValue}
+
+import org.apache.spark.{SparkContext, TaskContext}
+import org.apache.spark.rdd.RDD
+import org.apache.spark.sql.Row
+
+package object implicits {
+
+  implicit def toRichRowIterator(it: Iterator[Row]): RichRowIterator = new RichRowIterator(it)
+
+  implicit def toRichPairRDD[K, V](r: RDD[(K, V)]): RichPairRDD[K, V] = new RichPairRDD(r)
+
+  implicit def toRichRDD[T](r: RDD[T]): RichRDD[T] = new RichRDD(r)
+
+  implicit def toRichContextRDDRegionValue(r: ContextRDD[RegionValue]): RichContextRDDRegionValue =
+    new RichContextRDDRegionValue(r)
+
+  implicit def toRichContextRDD[A](r: ContextRDD[A]): RichContextRDD[A] =
+    new RichContextRDD(r)
+
+  implicit def toRichContextRDDPair[K, V](r: ContextRDD[(K, V)]): RichContextRDDPair[K, V] =
+    new RichContextRDDPair(r)
+
+  implicit def toRichContextRDDLong(r: ContextRDD[Long]): RichContextRDDLong =
+    new RichContextRDDLong(r)
+
+  implicit def toRichContextRDDRow(r: ContextRDD[Row]): RichContextRDDRow =
+    new RichContextRDDRow(r)
+
+  implicit def toRichRow(r: Row): RichRow = new RichRow(r)
+
+  implicit def toRichSC(sc: SparkContext): RichSparkContext = new RichSparkContext(sc)
+
+  implicit def toRichTaskContext(ctx: TaskContext): RichTaskContext =
+    new RichTaskContext(ctx)
+
+  implicit def toRichJoinedRegionValue(jrv: JoinedRegionValue): RichJoinedRegionValue =
+    new RichJoinedRegionValue(jrv)
+}
diff --git a/hail/hail/src/is/hail/stats/LeveneHaldane.scala b/hail/hail/src/is/hail/stats/LeveneHaldane.scala
index 515b8085c08..e3dbb57a663 100644
--- a/hail/hail/src/is/hail/stats/LeveneHaldane.scala
+++ b/hail/hail/src/is/hail/stats/LeveneHaldane.scala
@@ -21,7 +21,7 @@ class LeveneHaldane(
 ) extends AbstractIntegerDistribution(rng) {
 
   // The probability mass function P(nAB), computing no more than necessary
-  def probability(nAB: Int): Double =
+  override def probability(nAB: Int): Double =
     if (nAB < 0 || nAB > nA || nAB % 2 != nA % 2)
       0.0
     else if (nAB >= mode)
@@ -47,7 +47,7 @@ class LeveneHaldane(
     }
 
   // P(nAB <= n1)
-  def cumulativeProbability(n1: Int): Double =
+  override def cumulativeProbability(n1: Int): Double =
     cumulativeProbability(-1, n1)
 
   // P(nAB > n0)
@@ -81,14 +81,15 @@ class LeveneHaldane(
   }
 
   def nB: Int = 2 * n - nA
-  def getNumericalMean: Double = 1.0 * nA * nB / (2 * n - 1)
+  override def getNumericalMean: Double = 1.0 * nA * nB / (2 * n - 1)
 
-  def getNumericalVariance: Double =
+  override def getNumericalVariance: Double =
     1.0 * nA * nB / (2 * n - 1) * (1 + (nA - 1.0) * (nB - 1) / (2 * n - 3) - 1.0 * nA * nB / (2 * n - 1))
 
-  def isSupportConnected: Boolean = true // interpreted as restricted to the even or odd integers,
-  def getSupportUpperBound: Int = nA
-  def getSupportLowerBound: Int = nA % 2
+  override def isSupportConnected: Boolean =
+    true // interpreted as restricted to the even or odd integers,
+  override def getSupportUpperBound: Int = nA
+  override def getSupportLowerBound: Int = nA % 2
 }
 
 object LeveneHaldane {
diff --git a/hail/hail/src/is/hail/stats/LinearMixedModel.scala b/hail/hail/src/is/hail/stats/LinearMixedModel.scala
index 97a5377bf70..8637a5b514a 100644
--- a/hail/hail/src/is/hail/stats/LinearMixedModel.scala
+++ b/hail/hail/src/is/hail/stats/LinearMixedModel.scala
@@ -3,10 +3,12 @@ package is.hail.stats
 import is.hail.annotations.{BroadcastRow, Region, RegionValue, RegionValueBuilder}
 import is.hail.backend.ExecuteContext
 import is.hail.backend.spark.SparkTaskContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{TableIR, TableLiteral, TableValue}
 import is.hail.linalg.RowMatrix
 import is.hail.rvd.{RVD, RVDType}
 import is.hail.sparkextras.ContextRDD
+import is.hail.sparkextras.implicits.toRichContextRDDRegionValue
 import is.hail.types.physical.{PCanonicalStruct, PFloat64, PInt64}
 import is.hail.types.virtual.{TStruct, TableType}
 import is.hail.utils._
diff --git a/hail/hail/src/is/hail/stats/LogisticRegressionModel.scala b/hail/hail/src/is/hail/stats/LogisticRegressionModel.scala
index 93133f2d14d..56ad88aa118 100644
--- a/hail/hail/src/is/hail/stats/LogisticRegressionModel.scala
+++ b/hail/hail/src/is/hail/stats/LogisticRegressionModel.scala
@@ -61,7 +61,7 @@ object WaldTest extends GLMTest {
     ("fit", GLMFit.schema),
   )
 
-  def test(
+  override def test(
     X: DenseMatrix[Double],
     y: DenseVector[Double],
     nullFit: GLMFit,
@@ -102,7 +102,7 @@ case class WaldStats(
   z: DenseVector[Double],
   p: DenseVector[Double],
 ) extends GLMStats {
-  def addToRVB(rvb: RegionValueBuilder): Unit = {
+  override def addToRVB(rvb: RegionValueBuilder): Unit = {
     rvb.addDouble(b(-1))
     rvb.addDouble(se(-1))
     rvb.addDouble(z(-1))
@@ -118,7 +118,7 @@ object LikelihoodRatioTest extends GLMTest {
     ("fit", GLMFit.schema),
   )
 
-  def test(
+  override def test(
     X: DenseMatrix[Double],
     y: DenseVector[Double],
     nullFit: GLMFit,
@@ -149,7 +149,7 @@ object LikelihoodRatioTest extends GLMTest {
 }
 
 case class LikelihoodRatioStats(b: DenseVector[Double], chi2: Double, p: Double) extends GLMStats {
-  def addToRVB(rvb: RegionValueBuilder): Unit = {
+  override def addToRVB(rvb: RegionValueBuilder): Unit = {
     rvb.addDouble(b(-1))
     rvb.addDouble(chi2)
     rvb.addDouble(p)
@@ -164,7 +164,7 @@ object LogisticFirthTest extends GLMTest {
     ("fit", GLMFit.schema),
   )
 
-  def test(
+  override def test(
     X: DenseMatrix[Double],
     y: DenseVector[Double],
     nullFit: GLMFit,
@@ -201,7 +201,7 @@ object LogisticFirthTest extends GLMTest {
 }
 
 case class FirthStats(b: DenseVector[Double], chi2: Double, p: Double) extends GLMStats {
-  def addToRVB(rvb: RegionValueBuilder): Unit = {
+  override def addToRVB(rvb: RegionValueBuilder): Unit = {
     rvb.addDouble(b(-1))
     rvb.addDouble(chi2)
     rvb.addDouble(p)
@@ -214,7 +214,7 @@ object LogisticScoreTest extends GLMTest {
     ("p_value", TFloat64),
   )
 
-  def test(
+  override def test(
     X: DenseMatrix[Double],
     y: DenseVector[Double],
     nullFit: GLMFit,
@@ -264,7 +264,7 @@ object LogisticScoreTest extends GLMTest {
 }
 
 case class ScoreStats(chi2: Double, p: Double) extends GLMStats {
-  def addToRVB(rvb: RegionValueBuilder): Unit = {
+  override def addToRVB(rvb: RegionValueBuilder): Unit = {
     rvb.addDouble(chi2)
     rvb.addDouble(p)
   }
@@ -283,7 +283,7 @@ class LogisticRegressionModel(X: DenseMatrix[Double], y: DenseVector[Double])
   val n: Int = X.rows
   val m: Int = X.cols
 
-  def bInterceptOnly(): DenseVector[Double] = {
+  override def bInterceptOnly(): DenseVector[Double] = {
     require(m > 0)
     val b = DenseVector.zeros[Double](m)
     val avg = sum(y) / n
@@ -291,7 +291,7 @@ class LogisticRegressionModel(X: DenseMatrix[Double], y: DenseVector[Double])
     b
   }
 
-  def fit(optNullFit: Option[GLMFit] = None, maxIter: Int, tol: Double): GLMFit = {
+  override def fit(optNullFit: Option[GLMFit] = None, maxIter: Int, tol: Double): GLMFit = {
 
     val b = DenseVector.zeros[Double](m)
     val mu = DenseVector.zeros[Double](n)
diff --git a/hail/hail/src/is/hail/stats/PoissonRegressionModel.scala b/hail/hail/src/is/hail/stats/PoissonRegressionModel.scala
index 39e4a0dcc0c..1f9f3652549 100644
--- a/hail/hail/src/is/hail/stats/PoissonRegressionModel.scala
+++ b/hail/hail/src/is/hail/stats/PoissonRegressionModel.scala
@@ -15,7 +15,7 @@ object PoissonScoreTest extends GLMTest {
     ("p_value", TFloat64),
   )
 
-  def test(
+  override def test(
     X: DenseMatrix[Double],
     y: DenseVector[Double],
     nullFit: GLMFit,
@@ -71,7 +71,7 @@ class PoissonRegressionModel(X: DenseMatrix[Double], y: DenseVector[Double])
   val n: Int = X.rows
   val m: Int = X.cols
 
-  def bInterceptOnly(): DenseVector[Double] = {
+  override def bInterceptOnly(): DenseVector[Double] = {
     require(m > 0)
     val b = DenseVector.zeros[Double](m)
     val avg = sum(y) / n
@@ -79,7 +79,7 @@ class PoissonRegressionModel(X: DenseMatrix[Double], y: DenseVector[Double])
     b
   }
 
-  def fit(optNullFit: Option[GLMFit] = None, maxIter: Int, tol: Double): GLMFit = {
+  override def fit(optNullFit: Option[GLMFit] = None, maxIter: Int, tol: Double): GLMFit = {
 
     val b = DenseVector.zeros[Double](m)
     val mu = DenseVector.zeros[Double](n)
diff --git a/hail/hail/src/is/hail/stats/RegressionUtils.scala b/hail/hail/src/is/hail/stats/RegressionUtils.scala
index d3ec689bc6e..2a16dd8a9fc 100644
--- a/hail/hail/src/is/hail/stats/RegressionUtils.scala
+++ b/hail/hail/src/is/hail/stats/RegressionUtils.scala
@@ -1,7 +1,8 @@
 package is.hail.stats
 
 import is.hail.annotations.Region
-import is.hail.expr.ir.{IntArrayBuilder, MatrixValue}
+import is.hail.collection.IntArrayBuilder
+import is.hail.expr.ir.MatrixValue
 import is.hail.types.physical.{PArray, PStruct}
 import is.hail.types.virtual.TFloat64
 import is.hail.utils._
diff --git a/hail/hail/src/is/hail/stats/eigSymD.scala b/hail/hail/src/is/hail/stats/eigSymD.scala
index 2367330d9f3..fff342fd541 100644
--- a/hail/hail/src/is/hail/stats/eigSymD.scala
+++ b/hail/hail/src/is/hail/stats/eigSymD.scala
@@ -17,7 +17,7 @@ object eigSymD extends UFunc {
   type DenseEigSymD = EigSymD[DenseVector[Double], DenseMatrix[Double]]
 
   implicit object eigSymD_DM_Impl extends Impl[DenseMatrix[Double], DenseEigSymD] {
-    def apply(X: DenseMatrix[Double]): DenseEigSymD =
+    override def apply(X: DenseMatrix[Double]): DenseEigSymD =
       doeigSymD(X, rightEigenvectors = true) match {
         case (ev, Some(rev)) => EigSymD(ev, rev)
         case _ => throw new RuntimeException("Shouldn't be here!")
@@ -27,7 +27,7 @@ object eigSymD extends UFunc {
 
   object justEigenvalues extends UFunc {
     implicit object eigSymD_DM_Impl extends Impl[DenseMatrix[Double], DenseVector[Double]] {
-      def apply(X: DenseMatrix[Double]): DenseVector[Double] =
+      override def apply(X: DenseMatrix[Double]): DenseVector[Double] =
         doeigSymD(X, rightEigenvectors = false)._1
     }
 
@@ -84,7 +84,7 @@ object eigSymR extends UFunc {
   type DenseeigSymR = EigSymR[DenseVector[Double], DenseMatrix[Double]]
 
   implicit object eigSymR_DM_Impl extends Impl[DenseMatrix[Double], DenseeigSymR] {
-    def apply(X: DenseMatrix[Double]): DenseeigSymR =
+    override def apply(X: DenseMatrix[Double]): DenseeigSymR =
       doeigSymR(X, rightEigenvectors = true) match {
         case (ev, Some(rev)) => EigSymR(ev, rev)
         case _ => throw new RuntimeException("Shouldn't be here!")
@@ -94,7 +94,7 @@ object eigSymR extends UFunc {
 
   object justEigenvalues extends UFunc {
     implicit object eigSymR_DM_Impl extends Impl[DenseMatrix[Double], DenseVector[Double]] {
-      def apply(X: DenseMatrix[Double]): DenseVector[Double] =
+      override def apply(X: DenseMatrix[Double]): DenseVector[Double] =
         doeigSymR(X, rightEigenvectors = false)._1
     }
 
diff --git a/hail/hail/src/is/hail/stats/package.scala b/hail/hail/src/is/hail/stats/package.scala
index 88df128226d..c918df0e28f 100644
--- a/hail/hail/src/is/hail/stats/package.scala
+++ b/hail/hail/src/is/hail/stats/package.scala
@@ -1,5 +1,6 @@
 package is.hail
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.types.physical.{PCanonicalStruct, PFloat64}
 import is.hail.utils._
 
diff --git a/hail/hail/src/is/hail/types/Box.scala b/hail/hail/src/is/hail/types/Box.scala
index 3c516dd19df..96dc7165fe6 100644
--- a/hail/hail/src/is/hail/types/Box.scala
+++ b/hail/hail/src/is/hail/types/Box.scala
@@ -4,7 +4,7 @@ import java.util.function._
 
 final case class Box[T](
   b: ThreadLocal[Option[T]] = ThreadLocal.withInitial(
-    new Supplier[Option[T]] { def get = None }
+    new Supplier[Option[T]] { override def get = None }
   ),
   matchCond: (T, T) => Boolean = { (a: T, b: T) => a == b },
 ) {
diff --git a/hail/hail/src/is/hail/types/TypeWithRequiredness.scala b/hail/hail/src/is/hail/types/TypeWithRequiredness.scala
index 40aa288434f..e91ae89121c 100644
--- a/hail/hail/src/is/hail/types/TypeWithRequiredness.scala
+++ b/hail/hail/src/is/hail/types/TypeWithRequiredness.scala
@@ -2,6 +2,7 @@ package is.hail.types
 
 import is.hail.annotations.{Annotation, NDArray}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{ComputeUsesAndDefs, Env, IR}
 import is.hail.expr.ir.lowering.TableStage
 import is.hail.types.physical._
@@ -9,7 +10,7 @@ import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.concrete.SIndexablePointer
 import is.hail.types.physical.stypes.interfaces.{SBaseStruct, SInterval, SNDArray, SStream}
 import is.hail.types.virtual._
-import is.hail.utils.{toMapFast, FastSeq, Interval}
+import is.hail.utils.{toMapFast, Interval}
 
 import scala.collection.compat._
 
@@ -53,12 +54,6 @@ object BaseTypeWithRequiredness {
           assert(rf.index == f.index)
           check(rf.typ, f.typ)
         }
-      case r: RUnion =>
-        val union = typ.asInstanceOf[TUnion]
-        r.cases.lazyZip(union.cases).foreach { (rc, c) =>
-          assert(rc._1 == c.name)
-          check(rc._2, c.typ)
-        }
     }
   }
 }
@@ -74,7 +69,6 @@ object TypeWithRequiredness {
     case t: TInterval => RInterval(apply(t.pointType), apply(t.pointType))
     case t: TStruct => RStruct.fromNamesAndTypes(t.fields.map(f => f.name -> apply(f.typ)))
     case t: TTuple => RTuple.fromNamesAndTypes(t.fields.map(f => f.name -> apply(f.typ)))
-    case t: TUnion => RUnion(t.cases.map(c => c.name -> apply(c.typ)))
   }
 }
 
@@ -302,22 +296,24 @@ object RPrimitive {
 final case class RPrimitive() extends TypeWithRequiredness {
   val children: IndexedSeq[TypeWithRequiredness] = RPrimitive.children
 
-  def _unionLiteral(a: Annotation): Unit = ()
-  def _matchesPType(pt: PType): Boolean = RPrimitive.typeSupported(pt.virtualType)
-  def _unionPType(pType: PType): Unit = assert(RPrimitive.typeSupported(pType.virtualType))
-  def _unionEmitType(emitType: EmitType) = assert(RPrimitive.typeSupported(emitType.virtualType))
+  override def _unionLiteral(a: Annotation): Unit = ()
+  override def _matchesPType(pt: PType): Boolean = RPrimitive.typeSupported(pt.virtualType)
+  override def _unionPType(pType: PType): Unit = assert(RPrimitive.typeSupported(pType.virtualType))
+
+  override def _unionEmitType(emitType: EmitType) =
+    assert(RPrimitive.typeSupported(emitType.virtualType))
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RPrimitive = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RPrimitive = {
     assert(newChildren.isEmpty)
     RPrimitive()
   }
 
-  def canonicalPType(t: Type): PType = {
+  override def canonicalPType(t: Type): PType = {
     assert(RPrimitive.typeSupported(t))
     PType.canonical(t, required)
   }
 
-  def _toString: String = "RPrimitive"
+  override def _toString: String = "RPrimitive"
 }
 
 abstract class RContainer extends TypeWithRequiredness {
@@ -368,26 +364,26 @@ object RIterable {
 case class RIterable(elementType: TypeWithRequiredness, eltRequired: Boolean) extends RContainer {
   override val children: IndexedSeq[TypeWithRequiredness] = FastSeq(elementType)
 
-  def _unionLiteral(a: Annotation): Unit =
+  override def _unionLiteral(a: Annotation): Unit =
     a.asInstanceOf[Iterable[_]].foreach(elt => elementType.unionLiteral(elt))
 
-  def _matchesPType(pt: PType): Boolean =
+  override def _matchesPType(pt: PType): Boolean =
     elementType.matchesPType(tcoerce[PIterable](pt).elementType)
 
-  def _unionPType(pType: PType): Unit =
+  override def _unionPType(pType: PType): Unit =
     elementType.fromPType(pType.asInstanceOf[PIterable].elementType)
 
-  def _unionEmitType(emitType: EmitType): Unit =
+  override def _unionEmitType(emitType: EmitType): Unit =
     elementType.fromEmitType(emitType.st.asInstanceOf[SIndexablePointer].elementEmitType)
 
-  def _toString: String = s"RIterable[${elementType.toString}]"
+  override def _toString: String = s"RIterable[${elementType.toString}]"
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RIterable = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RIterable = {
     val IndexedSeq(newElt: TypeWithRequiredness) = newChildren
     RIterable(newElt)
   }
 
-  def canonicalPType(t: Type): PType = {
+  override def canonicalPType(t: Type): PType = {
     val elt = elementType.canonicalPType(tcoerce[TIterable](t).elementType)
     t match {
       case _: TArray => PCanonicalArray(elt, required = required)
@@ -404,11 +400,11 @@ case class RIterable(elementType: TypeWithRequiredness, eltRequired: Boolean) ex
 }
 
 case class RNDArray(elementType: TypeWithRequiredness) extends RContainer {
-  def eltRequired = true
+  override def eltRequired = true
 
   override val children: IndexedSeq[TypeWithRequiredness] = FastSeq(elementType)
 
-  def _unionLiteral(a: Annotation): Unit = {
+  override def _unionLiteral(a: Annotation): Unit = {
     val data = a.asInstanceOf[NDArray].getRowMajorElements()
     data.foreach { elt =>
       if (elt != null)
@@ -416,65 +412,65 @@ case class RNDArray(elementType: TypeWithRequiredness) extends RContainer {
     }
   }
 
-  def _matchesPType(pt: PType): Boolean =
+  override def _matchesPType(pt: PType): Boolean =
     elementType.matchesPType(tcoerce[PNDArray](pt).elementType)
 
-  def _unionPType(pType: PType): Unit =
+  override def _unionPType(pType: PType): Unit =
     elementType.fromPType(pType.asInstanceOf[PNDArray].elementType)
 
-  def _unionEmitType(emitType: EmitType): Unit =
+  override def _unionEmitType(emitType: EmitType): Unit =
     elementType.fromEmitType(emitType.st.asInstanceOf[SNDArray].elementEmitType)
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RNDArray = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RNDArray = {
     val IndexedSeq(newElt: TypeWithRequiredness) = newChildren
     RNDArray(newElt)
   }
 
-  def canonicalPType(t: Type): PType = {
+  override def canonicalPType(t: Type): PType = {
     val tnd = tcoerce[TNDArray](t)
     PCanonicalNDArray(elementType.canonicalPType(tnd.elementType), tnd.nDims, required = required)
   }
 
-  def _toString: String = s"RNDArray[${elementType.toString}]"
+  override def _toString: String = s"RNDArray[${elementType.toString}]"
 }
 
 case class RInterval(startType: TypeWithRequiredness, endType: TypeWithRequiredness)
     extends TypeWithRequiredness {
   val children: IndexedSeq[TypeWithRequiredness] = FastSeq(startType, endType)
 
-  def _unionLiteral(a: Annotation): Unit = {
+  override def _unionLiteral(a: Annotation): Unit = {
     startType.unionLiteral(a.asInstanceOf[Interval].start)
     endType.unionLiteral(a.asInstanceOf[Interval].end)
   }
 
-  def _matchesPType(pt: PType): Boolean =
+  override def _matchesPType(pt: PType): Boolean =
     startType.matchesPType(tcoerce[PInterval](pt).pointType) &&
       endType.matchesPType(tcoerce[PInterval](pt).pointType)
 
-  def _unionPType(pType: PType): Unit = {
+  override def _unionPType(pType: PType): Unit = {
     startType.fromPType(pType.asInstanceOf[PInterval].pointType)
     endType.fromPType(pType.asInstanceOf[PInterval].pointType)
   }
 
-  def _unionEmitType(emitType: EmitType): Unit = {
+  override def _unionEmitType(emitType: EmitType): Unit = {
     val sInterval = emitType.st.asInstanceOf[SInterval]
     startType.fromEmitType(sInterval.pointEmitType)
     endType.fromEmitType(sInterval.pointEmitType)
   }
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RInterval = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RInterval = {
     val IndexedSeq(newStart: TypeWithRequiredness, newEnd: TypeWithRequiredness) = newChildren
     RInterval(newStart, newEnd)
   }
 
-  def canonicalPType(t: Type): PType = t match {
+  override def canonicalPType(t: Type): PType = t match {
     case TInterval(pointType) =>
       val unified = startType.deepCopy().asInstanceOf[TypeWithRequiredness]
       unified.unionFrom(endType)
       PCanonicalInterval(unified.canonicalPType(pointType), required = required)
   }
 
-  def _toString: String = s"RInterval[${startType.toString}, ${endType.toString}]"
+  override def _toString: String = s"RInterval[${startType.toString}, ${endType.toString}]"
 }
 
 case class RField(name: String, typ: TypeWithRequiredness, index: Int)
@@ -484,7 +480,7 @@ sealed abstract class RBaseStruct extends TypeWithRequiredness {
   def size: Int = fields.length
   val children: IndexedSeq[TypeWithRequiredness] = fields.map(_.typ)
 
-  def _unionLiteral(a: Annotation): Unit = a match {
+  override def _unionLiteral(a: Annotation): Unit = a match {
     case a: Row => children.lazyZip(a.toSeq).foreach((r, f) => r.unionLiteral(f))
     case (k, v) =>
       // needed to handle the elements of a Map/Dict
@@ -493,13 +489,13 @@ sealed abstract class RBaseStruct extends TypeWithRequiredness {
       children(1).unionLiteral(v)
   }
 
-  def _matchesPType(pt: PType): Boolean =
+  override def _matchesPType(pt: PType): Boolean =
     tcoerce[PBaseStruct](pt).fields.forall(f => children(f.index).matchesPType(f.typ))
 
-  def _unionPType(pType: PType): Unit =
+  override def _unionPType(pType: PType): Unit =
     pType.asInstanceOf[PBaseStruct].fields.foreach(f => children(f.index).fromPType(f.typ))
 
-  def _unionEmitType(emitType: EmitType): Unit =
+  override def _unionEmitType(emitType: EmitType): Unit =
     emitType.st.asInstanceOf[SBaseStruct].fieldEmitTypes.zipWithIndex.foreach { case (et, idx) =>
       children(idx).fromEmitType(et)
     }
@@ -509,7 +505,7 @@ sealed abstract class RBaseStruct extends TypeWithRequiredness {
     fields.lazyZip(other.fields).foreach((fd1, fd2) => fd1.typ.unionFrom(fd2.typ))
   }
 
-  def canonicalPType(t: Type): PType = t match {
+  override def canonicalPType(t: Type): PType = t match {
     case ts: TStruct =>
       PCanonicalStruct(
         required = required,
@@ -536,7 +532,7 @@ case class RStruct(fields: IndexedSeq[RField]) extends RBaseStruct {
   def fieldOption(name: String): Option[TypeWithRequiredness] = fieldType.get(name)
   def hasField(name: String): Boolean = fieldType.contains(name)
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RStruct = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RStruct = {
     assert(newChildren.length == fields.length)
     RStruct.fromNamesAndTypes(Array.tabulate(fields.length)(i =>
       fields(i).name -> tcoerce[TypeWithRequiredness](newChildren(i))
@@ -546,7 +542,7 @@ case class RStruct(fields: IndexedSeq[RField]) extends RBaseStruct {
   def select(newFields: Array[String]): RStruct =
     RStruct(Array.tabulate(newFields.length)(i => RField(newFields(i), field(newFields(i)), i)))
 
-  def _toString: String =
+  override def _toString: String =
     s"RStruct[${fields.map(f => s"${f.name}: ${f.typ.toString}").mkString(",")}]"
 }
 
@@ -559,37 +555,17 @@ case class RTuple(fields: IndexedSeq[RField]) extends RBaseStruct {
   val fieldType: collection.Map[String, TypeWithRequiredness] = toMapFast(fields)(_.name, _.typ)
   def field(idx: Int): TypeWithRequiredness = fieldType(idx.toString)
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RTuple = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RTuple = {
     assert(newChildren.length == fields.length)
     RTuple(fields.lazyZip(newChildren).map { (f, c) =>
       RField(f.name, tcoerce[TypeWithRequiredness](c), f.index)
     })
   }
 
-  def _toString: String =
+  override def _toString: String =
     s"RTuple[${fields.map(f => s"${f.index}: ${f.typ.toString}").mkString(",")}]"
 }
 
-case class RUnion(cases: IndexedSeq[(String, TypeWithRequiredness)]) extends TypeWithRequiredness {
-  val children: IndexedSeq[TypeWithRequiredness] = cases.map(_._2)
-  def _unionLiteral(a: Annotation): Unit = ???
-  def _matchesPType(pt: PType): Boolean = ???
-  def _unionPType(pType: PType): Unit = ???
-  def _unionEmitType(emitType: EmitType): Unit = ???
-
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RUnion = {
-    assert(newChildren.length == cases.length)
-    RUnion(Array.tabulate(cases.length)(i =>
-      cases(i)._1 -> tcoerce[TypeWithRequiredness](newChildren(i))
-    ))
-  }
-
-  def canonicalPType(t: Type): PType = ???
-
-  def _toString: String =
-    s"RStruct[${cases.map { case (n, t) => s"$n: ${t.toString}" }.mkString(",")}]"
-}
-
 object RTable {
   def apply(rowStruct: RStruct, globStruct: RStruct, key: IndexedSeq[String]): RTable =
     RTable(
@@ -685,7 +661,7 @@ case class RTable(
 
   def changeKey(key: IndexedSeq[String]): RTable = RTable(rowFields, globalFields, key)
 
-  def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RTable = {
+  override def copy(newChildren: IndexedSeq[BaseTypeWithRequiredness]): RTable = {
     assert(newChildren.length == rowFields.length + globalFields.length)
     val newRowFields = rowFields.lazyZip(newChildren.take(rowFields.length)).map {
       case ((n, _), r: TypeWithRequiredness) => n -> r
diff --git a/hail/hail/src/is/hail/types/encoded/EArray.scala b/hail/hail/src/is/hail/types/encoded/EArray.scala
index 99b18b22bab..2265578cf3c 100644
--- a/hail/hail/src/is/hail/types/encoded/EArray.scala
+++ b/hail/hail/src/is/hail/types/encoded/EArray.scala
@@ -2,6 +2,9 @@ package is.hail.types.encoded
 
 import is.hail.annotations.{Region, UnsafeUtils}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
@@ -9,11 +12,10 @@ import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
 import is.hail.types.virtual._
-import is.hail.utils._
 
 final case class EArray(val elementType: EType, override val required: Boolean = false)
     extends EContainer {
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TContainer].elementType)
     requestedType match {
       case _: TSet =>
@@ -193,7 +195,7 @@ final case class EArray(val elementType: EType, override val required: Boolean =
     new SIndexablePointerValue(st, array, len, cb.memoize(arrayType.firstElementOffset(array, len)))
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
     val skip = elementType.buildSkip(cb.emb.ecb)
     val len = cb.newLocal[Int]("len", in.readInt())
     val i = cb.newLocal[Int]("i")
@@ -212,8 +214,8 @@ final case class EArray(val elementType: EType, override val required: Boolean =
     }
   }
 
-  def _asIdent = s"array_of_${elementType.asIdent}"
-  def _toPretty = s"EArray[$elementType]"
+  override def _asIdent = s"array_of_${elementType.asIdent}"
+  override def _toPretty = s"EArray[$elementType]"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "EArray["
@@ -221,5 +223,5 @@ final case class EArray(val elementType: EType, override val required: Boolean =
     sb += ']'
   }
 
-  def setRequired(newRequired: Boolean): EArray = EArray(elementType, newRequired)
+  override def setRequired(newRequired: Boolean): EArray = EArray(elementType, newRequired)
 }
diff --git a/hail/hail/src/is/hail/types/encoded/EBaseStruct.scala b/hail/hail/src/is/hail/types/encoded/EBaseStruct.scala
index 40b4602f903..6c306ee09ac 100644
--- a/hail/hail/src/is/hail/types/encoded/EBaseStruct.scala
+++ b/hail/hail/src/is/hail/types/encoded/EBaseStruct.scala
@@ -2,6 +2,8 @@ package is.hail.types.encoded
 
 import is.hail.annotations.{Region, UnsafeUtils}
 import is.hail.asm4s.{Field => _, _}
+import is.hail.asm4s.implicits._
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.BaseStruct
@@ -11,6 +13,7 @@ import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces.{SBaseStructValue, SLocus, SLocusValue}
 import is.hail.types.virtual._
 import is.hail.utils._
+import is.hail.utils.implicits.{toRichBoolean, toTruncatable}
 
 final case class EField(name: String, typ: EType, index: Int) {
   def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
@@ -55,7 +58,7 @@ final case class EBaseStruct(fields: IndexedSeq[EField], override val required:
     )
   }
 
-  def _decodedSType(requestedType: Type): SType = requestedType match {
+  override def _decodedSType(requestedType: Type): SType = requestedType match {
     case t: TInterval =>
       val structPType = decodedPType(t.structRepresentation).asInstanceOf[PStruct]
       val pointType = structPType.field("start").typ
@@ -198,7 +201,7 @@ final case class EBaseStruct(fields: IndexedSeq[EField], override val required:
     }
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
     val mbytes = cb.newLocal[Long]("mbytes", r.allocate(const(1L), const(nMissingBytes.toLong)))
     cb += in.readBytes(r, mbytes, nMissingBytes)
     fields.foreach { f =>
@@ -210,7 +213,7 @@ final case class EBaseStruct(fields: IndexedSeq[EField], override val required:
     }
   }
 
-  def _asIdent: String = {
+  override def _asIdent: String = {
     val sb = new StringBuilder
     sb ++= "struct_of_"
     types.foreachBetween(sb ++= _.asIdent)(sb ++= "AND")
@@ -218,7 +221,7 @@ final case class EBaseStruct(fields: IndexedSeq[EField], override val required:
     sb.result()
   }
 
-  def _toPretty: String = {
+  override def _toPretty: String = {
     val sb = new StringBuilder
     _pretty(sb, 0, compact = true)
     sb.result()
@@ -237,5 +240,5 @@ final case class EBaseStruct(fields: IndexedSeq[EField], override val required:
       sb += '\n' ++= " " * indent += '}': Unit
     }
 
-  def setRequired(newRequired: Boolean): EBaseStruct = EBaseStruct(fields, newRequired)
+  override def setRequired(newRequired: Boolean): EBaseStruct = EBaseStruct(fields, newRequired)
 }
diff --git a/hail/hail/src/is/hail/types/encoded/EBinary.scala b/hail/hail/src/is/hail/types/encoded/EBinary.scala
index e82016973be..42f40fe4767 100644
--- a/hail/hail/src/is/hail/types/encoded/EBinary.scala
+++ b/hail/hail/src/is/hail/types/encoded/EBinary.scala
@@ -2,6 +2,7 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
@@ -9,7 +10,6 @@ import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces.{SBinary, SBinaryValue, SString}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EBinaryOptional extends EBinary(false)
 case object EBinaryRequired extends EBinary(true)
@@ -61,18 +61,18 @@ class EBinary(override val required: Boolean) extends EType {
     }
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipBytes(in.readInt())
 
-  def _decodedSType(requestedType: Type): SType = requestedType match {
+  override def _decodedSType(requestedType: Type): SType = requestedType match {
     case TBinary => SBinaryPointer(PCanonicalBinary(false))
     case TString => SStringPointer(PCanonicalString(false))
   }
 
-  def _asIdent = "binary"
-  def _toPretty = "EBinary"
+  override def _asIdent = "binary"
+  override def _toPretty = "EBinary"
 
-  def setRequired(newRequired: Boolean): EBinary = EBinary(newRequired)
+  override def setRequired(newRequired: Boolean): EBinary = EBinary(newRequired)
 }
 
 object EBinary {
diff --git a/hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala b/hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala
index be1fe202e80..1d3088f9c66 100644
--- a/hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala
+++ b/hail/hail/src/is/hail/types/encoded/EBlockMatrixNDArray.scala
@@ -2,6 +2,8 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
@@ -9,7 +11,6 @@ import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.SNDArrayPointer
 import is.hail.types.physical.stypes.interfaces.SNDArrayValue
 import is.hail.types.virtual._
-import is.hail.utils._
 
 final case class EBlockMatrixNDArray(
   elementType: EType,
@@ -18,10 +19,10 @@ final case class EBlockMatrixNDArray(
 ) extends EType {
   type DecodedPType = PCanonicalNDArray
 
-  def setRequired(newRequired: Boolean): EBlockMatrixNDArray =
+  override def setRequired(newRequired: Boolean): EBlockMatrixNDArray =
     EBlockMatrixNDArray(elementType, newRequired)
 
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TNDArray].elementType)
     SNDArrayPointer(PCanonicalNDArray(elementPType, 2, false))
   }
@@ -108,7 +109,7 @@ final case class EBlockMatrixNDArray(
     tFinisher(cb)
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
     val skip = elementType.buildSkip(cb.emb.ecb)
 
     val len = cb.newLocal[Int]("len", in.readInt() * in.readInt())
@@ -120,7 +121,7 @@ final case class EBlockMatrixNDArray(
   override def _asIdent: String =
     s"bm_ndarray_${if (encodeRowMajor) "row" else "column"}_major_of_${elementType.asIdent}"
 
-  def _toPretty = s"ENDArray[$elementType]"
+  override def _toPretty = s"ENDArray[$elementType]"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "ENDArray["
diff --git a/hail/hail/src/is/hail/types/encoded/EBoolean.scala b/hail/hail/src/is/hail/types/encoded/EBoolean.scala
index 744f9e7938d..0511bbacc63 100644
--- a/hail/hail/src/is/hail/types/encoded/EBoolean.scala
+++ b/hail/hail/src/is/hail/types/encoded/EBoolean.scala
@@ -2,12 +2,12 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.primitives.{SBoolean, SBooleanValue}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EBooleanOptional extends EBoolean(false)
 
@@ -25,16 +25,16 @@ class EBoolean(override val required: Boolean) extends EType {
   ): SValue =
     new SBooleanValue(cb.memoize(in.readBoolean()))
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipBoolean()
 
-  def _decodedSType(requestedType: Type): SType = SBoolean
+  override def _decodedSType(requestedType: Type): SType = SBoolean
 
-  def _asIdent = "bool"
+  override def _asIdent = "bool"
 
-  def _toPretty = "EBoolean"
+  override def _toPretty = "EBoolean"
 
-  def setRequired(newRequired: Boolean): EBoolean = EBoolean(newRequired)
+  override def setRequired(newRequired: Boolean): EBoolean = EBoolean(newRequired)
 }
 
 object EBoolean {
diff --git a/hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala b/hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
index a6e77e60812..b79c09e768d 100644
--- a/hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
+++ b/hail/hail/src/is/hail/types/encoded/EDictAsUnsortedArrayOfPairs.scala
@@ -2,13 +2,13 @@ package is.hail.types.encoded
 
 import is.hail.annotations._
 import is.hail.asm4s._
-import is.hail.expr.ir.{ArraySorter, EmitCodeBuilder, EmitRegion, StagedArrayBuilder}
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.expr.ir.{ArraySorter, EmitCodeBuilder, StagedArrayBuilder}
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{SType, SValue, SingleCodeType}
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 final case class EDictAsUnsortedArrayOfPairs(
   val elementType: EType,
@@ -18,7 +18,7 @@ final case class EDictAsUnsortedArrayOfPairs(
 
   private[this] val arrayRepr = EArray(elementType, required)
 
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TContainer].elementType)
     requestedType match {
       case _: TDict =>
@@ -27,13 +27,17 @@ final case class EDictAsUnsortedArrayOfPairs(
     }
   }
 
-  def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit =
+  override def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit =
     // Anything we have to encode from a region should already be sorted so we don't
     // have to do anything else
     arrayRepr._buildEncoder(cb, v, out)
 
-  def _buildDecoder(cb: EmitCodeBuilder, t: Type, region: Value[Region], in: Value[InputBuffer])
-    : SValue = {
+  override def _buildDecoder(
+    cb: EmitCodeBuilder,
+    t: Type,
+    region: Value[Region],
+    in: Value[InputBuffer],
+  ): SValue = {
     val tmpRegion = cb.memoize(Region.stagedCreate(Region.REGULAR, region.getPool()), "tmp_region")
 
     val arrayDecoder = arrayRepr.buildDecoder(t, cb.emb.ecb)
@@ -46,7 +50,7 @@ final case class EDictAsUnsortedArrayOfPairs(
       ab.add(cb, ab.elt.coerceSCode(cb, res, region, false).code)
     }
 
-    val sorter = new ArraySorter(EmitRegion(cb.emb, region), ab)
+    val sorter = new ArraySorter(cb.emb, region, ab)
     def lessThan(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_])
       : Value[Boolean] = {
       val lk = cb.memoize(sct.loadToSValue(cb, l).asBaseStruct.loadField(cb, 0))
@@ -64,12 +68,12 @@ final case class EDictAsUnsortedArrayOfPairs(
     ret
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     arrayRepr._buildSkip(cb, r, in)
 
-  def _asIdent = s"dict_of_${elementType.asIdent}"
-  def _toPretty = s"EDictAsUnsortedArrayOfPairs[$elementType]"
+  override def _asIdent = s"dict_of_${elementType.asIdent}"
+  override def _toPretty = s"EDictAsUnsortedArrayOfPairs[$elementType]"
 
-  def setRequired(newRequired: Boolean): EType =
+  override def setRequired(newRequired: Boolean): EType =
     EDictAsUnsortedArrayOfPairs(elementType, newRequired)
 }
diff --git a/hail/hail/src/is/hail/types/encoded/EFloat32.scala b/hail/hail/src/is/hail/types/encoded/EFloat32.scala
index 3442bb5840a..a8cf3175cf4 100644
--- a/hail/hail/src/is/hail/types/encoded/EFloat32.scala
+++ b/hail/hail/src/is/hail/types/encoded/EFloat32.scala
@@ -2,12 +2,12 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.primitives.{SFloat32, SFloat32Value}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EFloat32Optional extends EFloat32(false)
 
@@ -25,16 +25,16 @@ class EFloat32(override val required: Boolean) extends EType {
   ): SValue =
     new SFloat32Value(cb.memoize(in.readFloat()))
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipFloat()
 
-  def _decodedSType(requestedType: Type): SType = SFloat32
+  override def _decodedSType(requestedType: Type): SType = SFloat32
 
-  def _asIdent = "float32"
+  override def _asIdent = "float32"
 
-  def _toPretty = "EFloat32"
+  override def _toPretty = "EFloat32"
 
-  def setRequired(newRequired: Boolean): EFloat32 = EFloat32(newRequired)
+  override def setRequired(newRequired: Boolean): EFloat32 = EFloat32(newRequired)
 }
 
 object EFloat32 {
diff --git a/hail/hail/src/is/hail/types/encoded/EFloat64.scala b/hail/hail/src/is/hail/types/encoded/EFloat64.scala
index 05aabe2a1bd..1e04ede4cb9 100644
--- a/hail/hail/src/is/hail/types/encoded/EFloat64.scala
+++ b/hail/hail/src/is/hail/types/encoded/EFloat64.scala
@@ -2,12 +2,12 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.primitives.{SFloat64, SFloat64Value}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EFloat64Optional extends EFloat64(false)
 
@@ -25,16 +25,16 @@ class EFloat64(override val required: Boolean) extends EType {
   ): SValue =
     new SFloat64Value(cb.memoize(in.readDouble()))
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipDouble()
 
-  def _decodedSType(requestedType: Type): SType = SFloat64
+  override def _decodedSType(requestedType: Type): SType = SFloat64
 
-  def _asIdent = "float64"
+  override def _asIdent = "float64"
 
-  def _toPretty = "EFloat64"
+  override def _toPretty = "EFloat64"
 
-  def setRequired(newRequired: Boolean): EFloat64 = EFloat64(newRequired)
+  override def setRequired(newRequired: Boolean): EFloat64 = EFloat64(newRequired)
 }
 
 object EFloat64 {
diff --git a/hail/hail/src/is/hail/types/encoded/EInt32.scala b/hail/hail/src/is/hail/types/encoded/EInt32.scala
index b559261b162..7620d257ae0 100644
--- a/hail/hail/src/is/hail/types/encoded/EInt32.scala
+++ b/hail/hail/src/is/hail/types/encoded/EInt32.scala
@@ -2,15 +2,14 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
-import is.hail.types.physical._
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.{SCanonicalCall, SCanonicalCallValue}
 import is.hail.types.physical.stypes.interfaces.{SCall, SCallValue}
 import is.hail.types.physical.stypes.primitives.{SInt32, SInt32Value}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EInt32Optional extends EInt32(false)
 
@@ -38,26 +37,19 @@ class EInt32(override val required: Boolean) extends EType {
     }
   }
 
-  def _buildFundamentalDecoder(
-    cb: EmitCodeBuilder,
-    pt: PType,
-    region: Value[Region],
-    in: Value[InputBuffer],
-  ): Code[Int] = in.readInt()
-
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipInt()
 
-  def _decodedSType(requestedType: Type): SType = requestedType match {
+  override def _decodedSType(requestedType: Type): SType = requestedType match {
     case TCall => SCanonicalCall
     case _ => SInt32
   }
 
-  def _asIdent = "int32"
+  override def _asIdent = "int32"
 
-  def _toPretty = "EInt32"
+  override def _toPretty = "EInt32"
 
-  def setRequired(newRequired: Boolean): EInt32 = EInt32(newRequired)
+  override def setRequired(newRequired: Boolean): EInt32 = EInt32(newRequired)
 }
 
 object EInt32 {
diff --git a/hail/hail/src/is/hail/types/encoded/EInt64.scala b/hail/hail/src/is/hail/types/encoded/EInt64.scala
index b88517bcc02..26c5d66bf1f 100644
--- a/hail/hail/src/is/hail/types/encoded/EInt64.scala
+++ b/hail/hail/src/is/hail/types/encoded/EInt64.scala
@@ -2,12 +2,12 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.primitives.{SInt64, SInt64Value}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 case object EInt64Optional extends EInt64(false)
 
@@ -25,16 +25,16 @@ class EInt64(override val required: Boolean) extends EType {
   ): SValue =
     new SInt64Value(cb.memoize(in.readLong()))
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     cb += in.skipLong()
 
-  def _decodedSType(requestedType: Type): SType = SInt64
+  override def _decodedSType(requestedType: Type): SType = SInt64
 
-  def _asIdent = "int64"
+  override def _asIdent = "int64"
 
-  def _toPretty = "EInt64"
+  override def _toPretty = "EInt64"
 
-  def setRequired(newRequired: Boolean): EInt64 = EInt64(newRequired)
+  override def setRequired(newRequired: Boolean): EInt64 = EInt64(newRequired)
 }
 
 object EInt64 {
diff --git a/hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala b/hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala
index d6b505c44f4..569ce23b3dd 100644
--- a/hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala
+++ b/hail/hail/src/is/hail/types/encoded/ENDArrayColumnMajor.scala
@@ -2,6 +2,7 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.PCanonicalNDArray
@@ -9,7 +10,6 @@ import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.SNDArrayPointer
 import is.hail.types.physical.stypes.interfaces.{SNDArray, SNDArrayValue}
 import is.hail.types.virtual.{TNDArray, Type}
-import is.hail.utils._
 
 case class ENDArrayColumnMajor(elementType: EType, nDims: Int, required: Boolean = false)
     extends EContainer {
@@ -62,7 +62,7 @@ case class ENDArrayColumnMajor(elementType: EType, nDims: Int, required: Boolean
     pndFinisher(cb)
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
     val skip = elementType.buildSkip(cb.emb.ecb)
 
     val numElements = cb.newLocal[Long](
@@ -73,7 +73,7 @@ case class ENDArrayColumnMajor(elementType: EType, nDims: Int, required: Boolean
     cb.for_(cb.assign(i, 0L), i < numElements, cb.assign(i, i + 1L), skip(cb, r, in))
   }
 
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     val requestedTNDArray = requestedType.asInstanceOf[TNDArray]
     val elementPType = elementType.decodedPType(requestedTNDArray.elementType)
     SNDArrayPointer(PCanonicalNDArray(elementPType, requestedTNDArray.nDims, false))
diff --git a/hail/hail/src/is/hail/types/encoded/ENumpyBinaryNDArray.scala b/hail/hail/src/is/hail/types/encoded/ENumpyBinaryNDArray.scala
deleted file mode 100644
index e3e5a015e14..00000000000
--- a/hail/hail/src/is/hail/types/encoded/ENumpyBinaryNDArray.scala
+++ /dev/null
@@ -1,96 +0,0 @@
-package is.hail.types.encoded
-
-import is.hail.annotations.Region
-import is.hail.asm4s._
-import is.hail.expr.ir.EmitCodeBuilder
-import is.hail.io.{InputBuffer, OutputBuffer}
-import is.hail.types.physical.PCanonicalNDArray
-import is.hail.types.physical.stypes.{SType, SValue}
-import is.hail.types.physical.stypes.concrete.SNDArrayPointer
-import is.hail.types.physical.stypes.interfaces.SNDArrayValue
-import is.hail.types.physical.stypes.primitives.SFloat64
-import is.hail.types.virtual.{TNDArray, Type}
-import is.hail.utils.FastSeq
-
-// FIXME numpy format should not be a hail native serialized format, move this to ValueReader/Writer
-final case class ENumpyBinaryNDArray(nRows: Long, nCols: Long, required: Boolean) extends EType {
-  type DecodedPType = PCanonicalNDArray
-  val elementType = EFloat64(true)
-
-  def setRequired(newRequired: Boolean): ENumpyBinaryNDArray =
-    ENumpyBinaryNDArray(nRows, nCols, newRequired)
-
-  def _decodedSType(requestedType: Type): SType = {
-    val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TNDArray].elementType)
-    SNDArrayPointer(PCanonicalNDArray(elementPType, 2, false))
-  }
-
-  override def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit = {
-    val ndarray = v.asInstanceOf[SNDArrayValue]
-    assert(ndarray.st.elementType == SFloat64)
-    val i = cb.newLocal[Long]("i")
-    val j = cb.newLocal[Long]("j")
-    val writeElemF = elementType.buildEncoder(ndarray.st.elementType, cb.emb.ecb)
-
-    cb.for_(
-      cb.assign(i, 0L),
-      i < nRows,
-      cb.assign(i, i + 1L),
-      cb.for_(
-        cb.assign(j, 0L),
-        j < nCols,
-        cb.assign(j, j + 1L),
-        writeElemF(cb, ndarray.loadElement(FastSeq(i, j), cb), out),
-      ),
-    )
-
-  }
-
-  override def _buildDecoder(
-    cb: EmitCodeBuilder,
-    t: Type,
-    region: Value[Region],
-    in: Value[InputBuffer],
-  ): SValue = {
-    val st = decodedSType(t).asInstanceOf[SNDArrayPointer]
-    val pt = st.pType
-    val readElemF = elementType.buildInplaceDecoder(pt.elementType, cb.emb.ecb)
-
-    val stride0 = cb.newLocal[Long]("stride0", nCols * pt.elementType.byteSize)
-    val stride1 = cb.newLocal[Long]("stride1", pt.elementType.byteSize)
-
-    val n = cb.newLocal[Long]("length", nRows * nCols)
-
-    val (tFirstElementAddress, tFinisher) =
-      pt.constructDataFunction(IndexedSeq(nRows, nCols), IndexedSeq(stride0, stride1), cb, region)
-    val currElementAddress =
-      cb.newLocal[Long]("eblockmatrix_ndarray_currElementAddress", tFirstElementAddress)
-
-    val i = cb.newLocal[Long]("i")
-    cb.for_(
-      cb.assign(i, 0L),
-      i < n,
-      cb.assign(i, i + 1L), {
-        readElemF(cb, region, currElementAddress, in)
-        cb.assign(currElementAddress, currElementAddress + pt.elementType.byteSize)
-      },
-    )
-
-    tFinisher(cb)
-  }
-
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
-    ???
-
-  override def _asIdent: String =
-    s"${nRows}by${nCols}_numpy_array_of_${elementType.asIdent}"
-
-  def _toPretty = s"ENDArray[$elementType]"
-
-  override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
-    sb ++= "ENDArray["
-    elementType.pretty(sb, indent, compact)
-    sb += ']'
-  }
-
-}
diff --git a/hail/hail/src/is/hail/types/encoded/ERNGState.scala b/hail/hail/src/is/hail/types/encoded/ERNGState.scala
index 71b7d70c8f6..7b19d24411a 100644
--- a/hail/hail/src/is/hail/types/encoded/ERNGState.scala
+++ b/hail/hail/src/is/hail/types/encoded/ERNGState.scala
@@ -2,6 +2,7 @@ package is.hail.types.encoded
 
 import is.hail.annotations.Region
 import is.hail.asm4s.Value
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical.stypes.SValue
@@ -9,7 +10,6 @@ import is.hail.types.physical.stypes.concrete.{
   SCanonicalRNGStateValue, SRNGState, SRNGStateStaticInfo, SRNGStateStaticSizeValue,
 }
 import is.hail.types.virtual.Type
-import is.hail.utils._
 
 //case object ERNGStateOptional extends ERNGState(false)
 //
@@ -54,7 +54,7 @@ final case class ERNGState(override val required: Boolean, staticInfo: Option[SR
       )
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     staticInfo match {
       case Some(staticInfo) =>
         for (_ <- 0 until (4 + staticInfo.numWordsInLastBlock))
@@ -67,11 +67,11 @@ final case class ERNGState(override val required: Boolean, staticInfo: Option[SR
         cb += in.skipInt()
     }
 
-  def _decodedSType(requestedType: Type): SRNGState = SRNGState(staticInfo)
+  override def _decodedSType(requestedType: Type): SRNGState = SRNGState(staticInfo)
 
-  def _asIdent = "rngstate"
+  override def _asIdent = "rngstate"
 
-  def _toPretty = "ERNGState"
+  override def _toPretty = "ERNGState"
 
-  def setRequired(newRequired: Boolean): ERNGState = ERNGState(newRequired, staticInfo)
+  override def setRequired(newRequired: Boolean): ERNGState = ERNGState(newRequired, staticInfo)
 }
diff --git a/hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala b/hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala
index 50a828445b6..778fdfffc63 100644
--- a/hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala
+++ b/hail/hail/src/is/hail/types/encoded/EStructOfArrays.scala
@@ -2,6 +2,10 @@ package is.hail.types.encoded
 
 import is.hail.annotations.{Region, UnsafeUtils}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{
+  valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer, valueToRichCodeRegion,
+}
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types._
@@ -10,7 +14,6 @@ import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.{Field => TField, _}
-import is.hail.utils._
 
 object EStructOfArrays {
   // expand this as more types are supported
@@ -72,14 +75,18 @@ final case class EStructOfArrays(
       )
   }
 
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     require(requestedType.isInstanceOf[TArray])
     val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TContainer].elementType)
     SIndexablePointer(PCanonicalArray(elementPType, required = false))
   }
 
-  def _buildDecoder(cb: EmitCodeBuilder, t: Type, region: Value[Region], in: Value[InputBuffer])
-    : SValue = {
+  override def _buildDecoder(
+    cb: EmitCodeBuilder,
+    t: Type,
+    region: Value[Region],
+    in: Value[InputBuffer],
+  ): SValue = {
     val st = tcoerce[SIndexablePointer](decodedSType(t))
     val pt = tcoerce[PCanonicalArray](st.pType)
     val ept = tcoerce[PBaseStruct](pt.elementType)
@@ -157,26 +164,27 @@ final case class EStructOfArrays(
     )
   }
 
-  def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit = v match {
-    case sv: SIndexablePointerValue =>
-      val pArray = sv.st.pType.asInstanceOf[PCanonicalArrayBackedContainer].arrayRep
-      val r: Value[Region] = // scratch region
-        cb.memoize(cb.emb.ecb.pool().invoke[Region]("getRegion"))
-      cb += out.writeInt(sv.length)
-      if (!elementType.required) {
-        val nMissingBytes = cb.memoize(pArray.nMissingBytes(sv.length))
-        cb += out.writeBytes(sv.a + pArray.missingBytesOffset, nMissingBytes)
-      }
+  override def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit =
+    v match {
+      case sv: SIndexablePointerValue =>
+        val pArray = sv.st.pType.asInstanceOf[PCanonicalArrayBackedContainer].arrayRep
+        val r: Value[Region] = // scratch region
+          cb.memoize(cb.emb.ecb.pool().invoke[Region]("getRegion"))
+        cb += out.writeInt(sv.length)
+        if (!elementType.required) {
+          val nMissingBytes = cb.memoize(pArray.nMissingBytes(sv.length))
+          cb += out.writeBytes(sv.a + pArray.missingBytesOffset, nMissingBytes)
+        }
 
-      fields.foreach { field =>
-        val pFieldType = tcoerce[PBaseStruct](pArray.elementType).fieldByName(field.name).typ
-        require(EStructOfArrays.supportsFieldType(pFieldType.virtualType))
-        val arrayType = PCanonicalArray(pFieldType, required = false)
-        transposeAndWriteField(cb, field, arrayType, sv, r, out)
-      }
+        fields.foreach { field =>
+          val pFieldType = tcoerce[PBaseStruct](pArray.elementType).fieldByName(field.name).typ
+          require(EStructOfArrays.supportsFieldType(pFieldType.virtualType))
+          val arrayType = PCanonicalArray(pFieldType, required = false)
+          transposeAndWriteField(cb, field, arrayType, sv, r, out)
+        }
 
-      cb += r.invalidate()
-  }
+        cb += r.invalidate()
+    }
 
   private[this] def transposeAndWriteField(
     cb: EmitCodeBuilder,
@@ -217,7 +225,7 @@ final case class EStructOfArrays(
     arrayEncoder(cb, arrayValue, out)
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit = {
     val length = cb.memoize(in.readInt())
     val nMissingBytes =
       cb.memoize(UnsafeUtils.packBitsToBytes(length)) // valid for all top level arrays
@@ -227,12 +235,12 @@ final case class EStructOfArrays(
     fields.foreach(field => field.typ.buildSkip(cb.emb.ecb)(cb, r, in))
   }
 
-  def setRequired(newRequired: Boolean): EStructOfArrays =
+  override def setRequired(newRequired: Boolean): EStructOfArrays =
     EStructOfArrays(fields, required = newRequired, structRequired = structRequired)
 
-  def _asIdent: String = s"struct_of_arrays_from_${elementType.asIdent}"
+  override def _asIdent: String = s"struct_of_arrays_from_${elementType.asIdent}"
 
-  def _toPretty: String = {
+  override def _toPretty: String = {
     val sb = new StringBuilder
     _pretty(sb, 0, compact = true)
     sb.result()
diff --git a/hail/hail/src/is/hail/types/encoded/EType.scala b/hail/hail/src/is/hail/types/encoded/EType.scala
index 0b002136582..f154cf1dd69 100644
--- a/hail/hail/src/is/hail/types/encoded/EType.scala
+++ b/hail/hail/src/is/hail/types/encoded/EType.scala
@@ -3,6 +3,7 @@ package is.hail.types.encoded
 import is.hail.annotations.Region
 import is.hail.asm4s.{coerce => _, _}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
   EmitClassBuilder, EmitCodeBuilder, EmitFunctionBuilder, EmitMethodBuilder, IRParser, ParamType,
   PunctuationToken, TokenIterator,
@@ -167,7 +168,7 @@ abstract class EType extends BaseType with Serializable with Requiredness {
 
   def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit
 
-  final def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
+  final override def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
     if (required)
       sb.append("+")
     _pretty(sb, indent, compact)
diff --git a/hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala b/hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala
index a8c85430c78..1f58fa470dd 100644
--- a/hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala
+++ b/hail/hail/src/is/hail/types/encoded/EUnsortedSet.scala
@@ -2,19 +2,19 @@ package is.hail.types.encoded
 
 import is.hail.annotations._
 import is.hail.asm4s._
-import is.hail.expr.ir.{ArraySorter, EmitCodeBuilder, EmitRegion, StagedArrayBuilder}
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.expr.ir.{ArraySorter, EmitCodeBuilder, StagedArrayBuilder}
 import is.hail.io.{InputBuffer, OutputBuffer}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{SType, SValue, SingleCodeType}
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 final case class EUnsortedSet(val elementType: EType, override val required: Boolean = false)
     extends EContainer {
   private[this] val arrayRepr = EArray(elementType, required)
 
-  def _decodedSType(requestedType: Type): SType = {
+  override def _decodedSType(requestedType: Type): SType = {
     val elementPType = elementType.decodedPType(requestedType.asInstanceOf[TContainer].elementType)
     requestedType match {
       case _: TSet =>
@@ -22,13 +22,17 @@ final case class EUnsortedSet(val elementType: EType, override val required: Boo
     }
   }
 
-  def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit =
+  override def _buildEncoder(cb: EmitCodeBuilder, v: SValue, out: Value[OutputBuffer]): Unit =
     // Anything we have to encode from a region should already be sorted so we don't
     // have to do anything else
     arrayRepr._buildEncoder(cb, v, out)
 
-  def _buildDecoder(cb: EmitCodeBuilder, t: Type, region: Value[Region], in: Value[InputBuffer])
-    : SValue = {
+  override def _buildDecoder(
+    cb: EmitCodeBuilder,
+    t: Type,
+    region: Value[Region],
+    in: Value[InputBuffer],
+  ): SValue = {
     val tmpRegion = cb.memoize(Region.stagedCreate(Region.REGULAR, region.getPool()), "tmp_region")
 
     val arrayDecoder = arrayRepr.buildDecoder(t, cb.emb.ecb)
@@ -41,7 +45,7 @@ final case class EUnsortedSet(val elementType: EType, override val required: Boo
       ab.add(cb, ab.elt.coerceSCode(cb, res, region, false).code)
     }
 
-    val sorter = new ArraySorter(EmitRegion(cb.emb, region), ab)
+    val sorter = new ArraySorter(cb.emb, region, ab)
     def lessThan(cb: EmitCodeBuilder, region: Value[Region], l: Value[_], r: Value[_])
       : Value[Boolean] =
       cb.emb.ecb.getOrdering(sct.loadedSType, sct.loadedSType)
@@ -55,10 +59,10 @@ final case class EUnsortedSet(val elementType: EType, override val required: Boo
     ret
   }
 
-  def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
+  override def _buildSkip(cb: EmitCodeBuilder, r: Value[Region], in: Value[InputBuffer]): Unit =
     arrayRepr._buildSkip(cb, r, in)
 
-  def _asIdent = s"set_of_${elementType.asIdent}"
-  def _toPretty = s"EUnsortedSet[$elementType]"
-  def setRequired(newRequired: Boolean): EType = EUnsortedSet(elementType, newRequired)
+  override def _asIdent = s"set_of_${elementType.asIdent}"
+  override def _toPretty = s"EUnsortedSet[$elementType]"
+  override def setRequired(newRequired: Boolean): EType = EUnsortedSet(elementType, newRequired)
 }
diff --git a/hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala b/hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala
index d7a053d34f5..2afee77ed19 100644
--- a/hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala
+++ b/hail/hail/src/is/hail/types/physical/PArrayBackedContainer.scala
@@ -96,10 +96,10 @@ trait PArrayBackedContainer extends PContainer {
   override def clearMissingBits(aoff: Long, length: Int) =
     arrayRep.clearMissingBits(aoff, length)
 
-  def contentsByteSize(length: Int): Long =
+  override def contentsByteSize(length: Int): Long =
     arrayRep.contentsByteSize(length)
 
-  def contentsByteSize(length: Code[Int]): Code[Long] =
+  override def contentsByteSize(length: Code[Int]): Code[Long] =
     arrayRep.contentsByteSize(length)
 
   override def initialize(aoff: Long, length: Int, setMissing: Boolean = false) =
@@ -215,5 +215,5 @@ trait PArrayBackedContainer extends PContainer {
 }
 
 trait PCanonicalArrayBackedContainer extends PArrayBackedContainer {
-  def arrayRep: PCanonicalArray
+  override def arrayRep: PCanonicalArray
 }
diff --git a/hail/hail/src/is/hail/types/physical/PBaseStruct.scala b/hail/hail/src/is/hail/types/physical/PBaseStruct.scala
index a84dc6b4c01..1cb8d2587f6 100644
--- a/hail/hail/src/is/hail/types/physical/PBaseStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/PBaseStruct.scala
@@ -3,9 +3,9 @@ package is.hail.types.physical
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.HailStateManager
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
-import is.hail.utils._
 
 object PBaseStruct {
   def alignment(types: Array[PType]): Long =
@@ -53,7 +53,7 @@ abstract class PBaseStruct extends PType {
 
   def identBase: String
 
-  def _asIdent: String = {
+  override def _asIdent: String = {
     val sb = new StringBuilder
     sb ++= identBase
     sb ++= "_of_"
@@ -79,7 +79,7 @@ abstract class PBaseStruct extends PType {
       types.zip(right.types).map { case (l, r) => l.unsafeOrdering(sm, r) }
 
     new UnsafeOrdering {
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
         var i = 0
         while (i < types.length) {
           val leftDefined = isFieldDefined(o1, i)
diff --git a/hail/hail/src/is/hail/types/physical/PBinary.scala b/hail/hail/src/is/hail/types/physical/PBinary.scala
index accb05d25ae..d7e92db3528 100644
--- a/hail/hail/src/is/hail/types/physical/PBinary.scala
+++ b/hail/hail/src/is/hail/types/physical/PBinary.scala
@@ -10,7 +10,7 @@ abstract class PBinary extends PType {
   lazy val virtualType: TBinary.type = TBinary
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int = {
+    override def compare(o1: Long, o2: Long): Int = {
       val l1 = loadLength(o1)
       val l2 = loadLength(o2)
 
diff --git a/hail/hail/src/is/hail/types/physical/PBoolean.scala b/hail/hail/src/is/hail/types/physical/PBoolean.scala
index 2d233a6dad2..f570c95f121 100644
--- a/hail/hail/src/is/hail/types/physical/PBoolean.scala
+++ b/hail/hail/src/is/hail/types/physical/PBoolean.scala
@@ -7,7 +7,7 @@ import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.primitives.{SBoolean, SBooleanValue}
 import is.hail.types.virtual.TBoolean
-import is.hail.utils.toRichBoolean
+import is.hail.utils.implicits.toRichBoolean
 
 case object PBooleanOptional extends PBoolean(false)
 case object PBooleanRequired extends PBoolean(true)
@@ -15,21 +15,21 @@ case object PBooleanRequired extends PBoolean(true)
 class PBoolean(override val required: Boolean) extends PType with PPrimitive {
   lazy val virtualType: TBoolean.type = TBoolean
 
-  def _asIdent = "bool"
+  override def _asIdent = "bool"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PBoolean"
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int =
+    override def compare(o1: Long, o2: Long): Int =
       java.lang.Boolean.compare(Region.loadBoolean(o1), Region.loadBoolean(o2))
   }
 
   override def byteSize: Long = 1
 
-  def sType: SBoolean.type = SBoolean
+  override def sType: SBoolean.type = SBoolean
 
-  def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
+  override def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
     cb += Region.storeBoolean(addr, value.asBoolean.value)
 
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBooleanValue =
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalArray.scala b/hail/hail/src/is/hail/types/physical/PCanonicalArray.scala
index 7e9b1a17d94..8079a918d11 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalArray.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalArray.scala
@@ -2,22 +2,22 @@ package is.hail.types.physical
 
 import is.hail.annotations._
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.codeToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
 import is.hail.types.virtual.{TArray, Type}
-import is.hail.utils._
 
 // This is a pointer array, whose byteSize is the size of its pointer
 final case class PCanonicalArray(elementType: PType, required: Boolean = false)
     extends PArray with PCanonicalArrayBackedContainer {
   assert(elementType.isRealizable)
 
-  def arrayRep = this
+  override def arrayRep = this
 
-  def _asIdent = s"array_of_${elementType.asIdent}"
+  override def _asIdent = s"array_of_${elementType.asIdent}"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "PCArray["
@@ -55,7 +55,7 @@ final case class PCanonicalArray(elementType: PType, required: Boolean = false)
 
   override val byteSize: Long = 8
 
-  def setRequired(required: Boolean): PCanonicalArray =
+  override def setRequired(required: Boolean): PCanonicalArray =
     if (required == this.required) this else PCanonicalArray(elementType, required)
 
   override def loadLength(aoff: Long): Int =
@@ -219,16 +219,16 @@ final case class PCanonicalArray(elementType: PType, required: Boolean = false)
       length,
     )
 
-    def hasNext: Boolean = i != length
-    def isDefined: Boolean = isElementDefined(aoff, i)
+    override def hasNext: Boolean = i != length
+    override def isDefined: Boolean = isElementDefined(aoff, i)
 
-    def value: Long =
+    override def value: Long =
       firstElementOffset + i * elementByteSize
 
-    def iterate(): Unit = i += 1
+    override def iterate(): Unit = i += 1
   }
 
-  def elementIterator(aoff: Long, length: Int): Iterator = new Iterator(aoff, length)
+  override def elementIterator(aoff: Long, length: Int): Iterator = new Iterator(aoff, length)
 
   override def allocate(region: Region, length: Int): Long =
     region.allocate(contentsAlignment, contentsByteSize(length))
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala b/hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala
index f9f1156cb11..8781b5d595b 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalBaseStruct.scala
@@ -2,6 +2,7 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region, UnsafeRow, UnsafeUtils}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.codeToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder}
 import is.hail.types.BaseStruct
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala b/hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala
index 88889112c89..42758d6390a 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalBinary.scala
@@ -2,18 +2,18 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.codeToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{SBinaryPointer, SBinaryPointerValue}
-import is.hail.utils._
 
 case object PCanonicalBinaryOptional extends PCanonicalBinary(false)
 
 case object PCanonicalBinaryRequired extends PCanonicalBinary(true)
 
 class PCanonicalBinary(val required: Boolean) extends PBinary {
-  def _asIdent = "binary"
+  override def _asIdent = "binary"
 
   override def copiedType: PType = this
 
@@ -53,48 +53,48 @@ class PCanonicalBinary(val required: Boolean) extends PBinary {
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PCBinary"
 
-  def contentAlignment: Long = 4
+  override def contentAlignment: Long = 4
 
-  def lengthHeaderBytes: Long = 4
+  override def lengthHeaderBytes: Long = 4
 
-  def contentByteSize(length: Int): Long = 4L + length
+  override def contentByteSize(length: Int): Long = 4L + length
 
-  def contentByteSize(length: Code[Int]): Code[Long] = (const(4) + length).toL
+  override def contentByteSize(length: Code[Int]): Code[Long] = (const(4) + length).toL
 
-  def allocate(region: Region, length: Int): Long =
+  override def allocate(region: Region, length: Int): Long =
     region.allocate(contentAlignment, contentByteSize(length))
 
-  def allocate(region: Code[Region], length: Code[Int]): Code[Long] =
+  override def allocate(region: Code[Region], length: Code[Int]): Code[Long] =
     region.allocate(const(contentAlignment), contentByteSize(length))
 
-  def loadLength(boff: Long): Int = Region.loadInt(boff)
+  override def loadLength(boff: Long): Int = Region.loadInt(boff)
 
-  def loadLength(boff: Code[Long]): Code[Int] = Region.loadInt(boff)
+  override def loadLength(boff: Code[Long]): Code[Int] = Region.loadInt(boff)
 
-  def loadBytes(bAddress: Code[Long], length: Code[Int]): Code[Array[Byte]] =
+  override def loadBytes(bAddress: Code[Long], length: Code[Int]): Code[Array[Byte]] =
     Region.loadBytes(this.bytesAddress(bAddress), length)
 
-  def loadBytes(bAddress: Code[Long]): Code[Array[Byte]] =
+  override def loadBytes(bAddress: Code[Long]): Code[Array[Byte]] =
     Code.memoize(bAddress, "pcbin_load_bytes_addr") { bAddress =>
       loadBytes(bAddress, this.loadLength(bAddress))
     }
 
-  def loadBytes(bAddress: Long, length: Int): Array[Byte] =
+  override def loadBytes(bAddress: Long, length: Int): Array[Byte] =
     Region.loadBytes(this.bytesAddress(bAddress), length)
 
-  def loadBytes(bAddress: Long): Array[Byte] =
+  override def loadBytes(bAddress: Long): Array[Byte] =
     this.loadBytes(bAddress, this.loadLength(bAddress))
 
-  def storeLength(boff: Long, len: Int): Unit = Region.storeInt(boff, len)
+  override def storeLength(boff: Long, len: Int): Unit = Region.storeInt(boff, len)
 
-  def storeLength(cb: EmitCodeBuilder, boff: Code[Long], len: Code[Int]): Unit =
+  override def storeLength(cb: EmitCodeBuilder, boff: Code[Long], len: Code[Int]): Unit =
     cb += Region.storeInt(boff, len)
 
-  def bytesAddress(boff: Long): Long = boff + lengthHeaderBytes
+  override def bytesAddress(boff: Long): Long = boff + lengthHeaderBytes
 
-  def bytesAddress(boff: Code[Long]): Code[Long] = boff + lengthHeaderBytes
+  override def bytesAddress(boff: Code[Long]): Code[Long] = boff + lengthHeaderBytes
 
-  def store(addr: Long, bytes: Array[Byte]): Unit = {
+  override def store(addr: Long, bytes: Array[Byte]): Unit = {
     Region.storeInt(addr, bytes.length)
     Region.storeBytes(bytesAddress(addr), bytes)
   }
@@ -163,12 +163,12 @@ class PCanonicalBinary(val required: Boolean) extends PBinary {
     }
   }
 
-  def sType: SBinaryPointer = SBinaryPointer(setRequired(false))
+  override def sType: SBinaryPointer = SBinaryPointer(setRequired(false))
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBinaryPointerValue =
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBinaryPointerValue =
     new SBinaryPointerValue(sType, cb.memoize(addr))
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     value.st match {
       case SBinaryPointer(PCanonicalBinary(_)) =>
@@ -191,7 +191,7 @@ class PCanonicalBinary(val required: Boolean) extends PBinary {
     }
   }
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -200,7 +200,7 @@ class PCanonicalBinary(val required: Boolean) extends PBinary {
   ): Unit =
     cb += Region.storeAddress(addr, store(cb, region, value, deepCopy))
 
-  def unstagedStoreAtAddress(
+  override def unstagedStoreAtAddress(
     sm: HailStateManager,
     addr: Long,
     region: Region,
@@ -212,10 +212,10 @@ class PCanonicalBinary(val required: Boolean) extends PBinary {
     Region.storeAddress(addr, copyFromAddress(sm, region, srcArray, srcAddress, deepCopy))
   }
 
-  def setRequired(required: Boolean): PCanonicalBinary =
+  override def setRequired(required: Boolean): PCanonicalBinary =
     if (required == this.required) this else PCanonicalBinary(required)
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = Region.loadAddress(addr)
+  override def loadFromNested(addr: Code[Long]): Code[Long] = Region.loadAddress(addr)
 
   override def unstagedLoadFromNested(addr: Long): Long = Region.loadAddress(addr)
 
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalCall.scala b/hail/hail/src/is/hail/types/physical/PCanonicalCall.scala
index c8c5bb49b05..91006d07d2a 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalCall.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalCall.scala
@@ -2,15 +2,15 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region, UnsafeOrdering}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{SCanonicalCall, SCanonicalCallValue}
 import is.hail.types.physical.stypes.interfaces.SCall
-import is.hail.utils._
 
 final case class PCanonicalCall(required: Boolean = false) extends PCall {
-  def _asIdent = "call"
+  override def _asIdent = "call"
 
   override def copiedType: PType = this
 
@@ -19,13 +19,13 @@ final case class PCanonicalCall(required: Boolean = false) extends PCall {
 
   val representation: PInt32 = PInt32(required)
 
-  def byteSize: Long = representation.byteSize
+  override def byteSize: Long = representation.byteSize
   override def alignment: Long = representation.alignment
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering =
     representation.unsafeOrdering(sm) // this was a terrible idea
 
-  def setRequired(required: Boolean) =
+  override def setRequired(required: Boolean) =
     if (required == this.required) this else PCanonicalCall(required)
 
   override def unstagedStoreAtAddress(
@@ -62,12 +62,12 @@ final case class PCanonicalCall(required: Boolean = false) extends PCall {
         representation._copyFromAddress(sm, region, pt.representation, srcAddress, deepCopy)
     }
 
-  def sType: SCall = SCanonicalCall
+  override def sType: SCall = SCanonicalCall
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SCanonicalCallValue =
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SCanonicalCallValue =
     new SCanonicalCallValue(cb.memoize(Region.loadInt(addr)))
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     value.st match {
       case SCanonicalCall =>
@@ -77,7 +77,7 @@ final case class PCanonicalCall(required: Boolean = false) extends PCall {
     }
   }
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -86,7 +86,7 @@ final case class PCanonicalCall(required: Boolean = false) extends PCall {
   ): Unit =
     cb += Region.storeInt(addr, value.asCall.canonicalCall(cb))
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = representation.loadFromNested(addr)
+  override def loadFromNested(addr: Code[Long]): Code[Long] = representation.loadFromNested(addr)
 
   override def unstagedLoadFromNested(addr: Long): Long =
     representation.unstagedLoadFromNested(addr)
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalDict.scala b/hail/hail/src/is/hail/types/physical/PCanonicalDict.scala
index 90c2c5e4f3d..908784f7e44 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalDict.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalDict.scala
@@ -23,10 +23,10 @@ final case class PCanonicalDict(keyType: PType, valueType: PType, required: Bool
 
   val arrayRep: PCanonicalArray = PCanonicalArray(elementType, required)
 
-  def setRequired(required: Boolean) =
+  override def setRequired(required: Boolean) =
     if (required == this.required) this else PCanonicalDict(keyType, valueType, required)
 
-  def _asIdent = s"dict_of_${keyType.asIdent}AND${valueType.asIdent}"
+  override def _asIdent = s"dict_of_${keyType.asIdent}AND${valueType.asIdent}"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "PCDict["
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala b/hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala
index 4e5db82dca3..4cd949494c5 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalInterval.scala
@@ -3,6 +3,7 @@ package is.hail.types.physical
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder}
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{
@@ -11,7 +12,7 @@ import is.hail.types.physical.stypes.concrete.{
 import is.hail.types.physical.stypes.interfaces.primitive
 import is.hail.types.physical.stypes.primitives.SBooleanValue
 import is.hail.types.virtual.{TInterval, Type}
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.utils.Interval
 
 import org.apache.spark.sql.Row
 
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala b/hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala
index 64f1fe78313..0bb34907ca2 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalLocus.scala
@@ -3,13 +3,13 @@ package is.hail.types.physical
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder}
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.{
   SCanonicalLocusPointer, SCanonicalLocusPointerValue, SStackStruct,
 }
 import is.hail.types.physical.stypes.interfaces._
-import is.hail.utils.FastSeq
 import is.hail.variant._
 
 object PCanonicalLocus {
@@ -27,19 +27,19 @@ object PCanonicalLocus {
 
 final case class PCanonicalLocus(rgName: String, required: Boolean = false) extends PLocus {
 
-  def byteSize: Long = representation.byteSize
+  override def byteSize: Long = representation.byteSize
   override def alignment: Long = representation.alignment
 
   override def copiedType: PType = this
 
-  def rg: String = rgName
+  override def rg: String = rgName
 
-  def _asIdent = s"locus_$rgName"
+  override def _asIdent = s"locus_$rgName"
 
   override def _pretty(sb: StringBuilder, indent: Call, compact: Boolean): Unit =
     sb ++= "PCLocus(" ++= rgName += ')': Unit
 
-  def setRequired(required: Boolean): PCanonicalLocus =
+  override def setRequired(required: Boolean): PCanonicalLocus =
     if (required == this.required) this else PCanonicalLocus(this.rgName, required)
 
   val representation: PCanonicalStruct = PCanonicalLocus.representation(required)
@@ -49,13 +49,14 @@ final case class PCanonicalLocus(rgName: String, required: Boolean = false) exte
 
   private[physical] def contigAddr(address: Long): Long = representation.loadField(address, 0)
 
-  def contig(address: Long): String = contigType.loadString(contigAddr(address))
-  def position(address: Long): Int = Region.loadInt(representation.fieldOffset(address, 1))
+  override def contig(address: Long): String = contigType.loadString(contigAddr(address))
+  override def position(address: Long): Int = Region.loadInt(representation.fieldOffset(address, 1))
 
   lazy val contigType: PCanonicalString =
     representation.field("contig").typ.asInstanceOf[PCanonicalString]
 
-  def position(off: Code[Long]): Code[Int] = Region.loadInt(representation.loadField(off, 1))
+  override def position(off: Code[Long]): Code[Int] =
+    Region.loadInt(representation.loadField(off, 1))
 
   lazy val positionType: PInt32 = representation.field("position").typ.asInstanceOf[PInt32]
 
@@ -65,7 +66,7 @@ final case class PCanonicalLocus(rgName: String, required: Boolean = false) exte
     val binaryOrd = representation.fieldType("contig").unsafeOrdering(sm)
 
     new UnsafeOrdering {
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
         val cOff1 = representation.loadField(o1, 0)
         val cOff2 = representation.loadField(o2, 0)
 
@@ -115,14 +116,15 @@ final case class PCanonicalLocus(rgName: String, required: Boolean = false) exte
         representation._copyFromAddress(sm, region, pt.representation, srcAddress, deepCopy)
     }
 
-  def sType: SCanonicalLocusPointer = SCanonicalLocusPointer(setRequired(false))
+  override def sType: SCanonicalLocusPointer = SCanonicalLocusPointer(setRequired(false))
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SCanonicalLocusPointerValue = {
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long])
+    : SCanonicalLocusPointerValue = {
     val a = cb.memoize(addr)
     new SCanonicalLocusPointerValue(sType, a, cb.memoize(contigAddr(a)), cb.memoize(position(a)))
   }
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     value.st match {
       case SCanonicalLocusPointer(pt) =>
@@ -139,7 +141,7 @@ final case class PCanonicalLocus(rgName: String, required: Boolean = false) exte
     }
   }
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -173,7 +175,7 @@ final case class PCanonicalLocus(rgName: String, required: Boolean = false) exte
     }
   }
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = addr
+  override def loadFromNested(addr: Code[Long]): Code[Long] = addr
 
   override def unstagedLoadFromNested(addr: Long): Long = addr
 
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala b/hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala
index 8f81ebe4fff..31b4b6c21da 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalNDArray.scala
@@ -2,7 +2,9 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, NDArray, Region, UnsafeOrdering}
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
   CodeParam, CodeParamType, EmitCode, EmitCodeBuilder, Param, ParamType, SCodeParam,
 }
@@ -10,7 +12,6 @@ import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.{TNDArray, Type}
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 
@@ -39,7 +40,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
 
   lazy val strideType: PCanonicalTuple = shapeType
 
-  def loadShape(ndAddr: Long, idx: Int): Long = {
+  override def loadShape(ndAddr: Long, idx: Int): Long = {
     val shapeTupleAddr = representation.loadField(ndAddr, 0)
     Region.loadLong(shapeType.loadField(shapeTupleAddr, idx))
   }
@@ -49,8 +50,11 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     Region.loadLong(strideType.loadField(shapeTupleAddr, idx))
   }
 
-  def loadShapes(cb: EmitCodeBuilder, addr: Value[Long], settables: IndexedSeq[Settable[Long]])
-    : Unit = {
+  override def loadShapes(
+    cb: EmitCodeBuilder,
+    addr: Value[Long],
+    settables: IndexedSeq[Settable[Long]],
+  ): Unit = {
     assert(settables.length == nDims, s"got ${settables.length} settables, expect $nDims dims")
     val shapeTuple = shapeType.loadCheapSCode(cb, representation.loadField(addr, "shape"))
     (0 until nDims).foreach { dimIdx =>
@@ -58,8 +62,11 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     }
   }
 
-  def loadStrides(cb: EmitCodeBuilder, addr: Value[Long], settables: IndexedSeq[Settable[Long]])
-    : Unit = {
+  override def loadStrides(
+    cb: EmitCodeBuilder,
+    addr: Value[Long],
+    settables: IndexedSeq[Settable[Long]],
+  ): Unit = {
     assert(settables.length == nDims)
     val strideTuple = strideType.loadCheapSCode(cb, representation.loadField(addr, "strides"))
     (0 until nDims).foreach { dimIdx =>
@@ -85,14 +92,16 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering =
     representation.unsafeOrdering(sm)
 
-  def numElements(shape: IndexedSeq[Value[Long]]): Code[Long] =
+  override def numElements(shape: IndexedSeq[Value[Long]]): Code[Long] =
     shape.foldLeft(1L: Code[Long])(_ * _)
 
   def numElements(shape: IndexedSeq[Long]): Long =
     shape.foldLeft(1L)(_ * _)
 
-  def makeColumnMajorStrides(sourceShapeArray: IndexedSeq[Value[Long]], cb: EmitCodeBuilder)
-    : IndexedSeq[Value[Long]] = {
+  override def makeColumnMajorStrides(
+    sourceShapeArray: IndexedSeq[Value[Long]],
+    cb: EmitCodeBuilder,
+  ): IndexedSeq[Value[Long]] = {
     val strides = new Array[Value[Long]](nDims)
     for (i <- 0 until nDims)
       if (i == 0) strides(i) = const(elementType.byteSize)
@@ -102,7 +111,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     strides
   }
 
-  def makeRowMajorStrides(sourceShapeArray: IndexedSeq[Value[Long]], cb: EmitCodeBuilder)
+  override def makeRowMajorStrides(sourceShapeArray: IndexedSeq[Value[Long]], cb: EmitCodeBuilder)
     : IndexedSeq[Value[Long]] = {
     val strides = new Array[Value[Long]](nDims)
     for (i <- (nDims - 1) to 0 by -1)
@@ -113,7 +122,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     strides
   }
 
-  def getElementAddress(indices: IndexedSeq[Long], nd: Long): Long = {
+  override def getElementAddress(indices: IndexedSeq[Long], nd: Long): Long = {
     var bytesAway = 0L
     indices.zipWithIndex.foreach { case (requestedIndex: Long, strideIndex: Int) =>
       bytesAway += requestedIndex * loadStride(nd, strideIndex)
@@ -168,8 +177,11 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     address
   }
 
-  def loadElement(cb: EmitCodeBuilder, indices: IndexedSeq[Value[Long]], ndAddress: Value[Long])
-    : SValue = {
+  override def loadElement(
+    cb: EmitCodeBuilder,
+    indices: IndexedSeq[Value[Long]],
+    ndAddress: Value[Long],
+  ): SValue = {
     val off = getElementAddress(cb, indices, ndAddress)
     elementType.loadCheapSCode(cb, elementType.loadFromNested(off))
   }
@@ -220,7 +232,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
       region,
     )
 
-  def constructByCopyingArray(
+  override def constructByCopyingArray(
     shape: IndexedSeq[Value[Long]],
     strides: IndexedSeq[Value[Long]],
     dataCode: SIndexableValue,
@@ -293,7 +305,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
       .coerceToShape(cb, newShape)
   }
 
-  def constructDataFunction(
+  override def constructDataFunction(
     shape: IndexedSeq[Value[Long]],
     strides: IndexedSeq[Value[Long]],
     cb: EmitCodeBuilder,
@@ -371,7 +383,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     )
   }
 
-  def _copyFromAddress(
+  override def _copyFromAddress(
     sm: HailStateManager,
     region: Region,
     srcPType: PType,
@@ -395,10 +407,10 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
   private def deepRenameNDArray(t: TNDArray) =
     PCanonicalNDArray(this.elementType.deepRename(t.elementType), this.nDims, this.required)
 
-  def setRequired(required: Boolean): PCanonicalNDArray =
+  override def setRequired(required: Boolean): PCanonicalNDArray =
     if (required == this.required) this else PCanonicalNDArray(elementType, nDims, required)
 
-  def unstagedStoreAtAddress(
+  override def unstagedStoreAtAddress(
     sm: HailStateManager,
     destAddress: Long,
     region: Region,
@@ -463,9 +475,9 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     }
   }
 
-  def sType: SNDArrayPointer = SNDArrayPointer(setRequired(false))
+  override def sType: SNDArrayPointer = SNDArrayPointer(setRequired(false))
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SNDArrayPointerValue = {
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SNDArrayPointerValue = {
     val a = cb.memoize(addr)
     val shapeTuple = shapeType.loadCheapSCode(cb, representation.loadField(a, "shape"))
     val shape =
@@ -478,14 +490,14 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
     new SNDArrayPointerValue(sType, a, shape, strides, firstDataAddress)
   }
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     val addr = cb.memoize(this.representation.allocate(region))
     storeAtAddress(cb, addr, region, value, deepCopy)
     addr
   }
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -548,7 +560,7 @@ final case class PCanonicalNDArray(elementType: PType, nDims: Int, required: Boo
   override def dataFirstElementPointer(ndAddr: Code[Long]): Code[Long] =
     Region.loadAddress(representation.loadField(ndAddr, "data"))
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = addr
+  override def loadFromNested(addr: Code[Long]): Code[Long] = addr
 
   override def unstagedLoadFromNested(addr: Long): Long = addr
 
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalSet.scala b/hail/hail/src/is/hail/types/physical/PCanonicalSet.scala
index f5f516672ab..5ae191292fb 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalSet.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalSet.scala
@@ -2,10 +2,10 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region}
 import is.hail.backend.HailStateManager
+import is.hail.collection.implicits.toRichIterable
 import is.hail.types.physical.stypes.concrete.{SIndexablePointer, SIndexablePointerValue}
 import is.hail.types.physical.stypes.interfaces.SIndexableValue
 import is.hail.types.virtual.{TSet, Type}
-import is.hail.utils._
 
 object PCanonicalSet {
   def coerceArrayCode(contents: SIndexableValue): SIndexableValue =
@@ -19,10 +19,10 @@ final case class PCanonicalSet(elementType: PType, required: Boolean = false)
     extends PSet with PCanonicalArrayBackedContainer {
   val arrayRep = PCanonicalArray(elementType, required)
 
-  def setRequired(required: Boolean) =
+  override def setRequired(required: Boolean) =
     if (required == this.required) this else PCanonicalSet(elementType, required)
 
-  def _asIdent = s"set_of_${elementType.asIdent}"
+  override def _asIdent = s"set_of_${elementType.asIdent}"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "PCSet["
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalString.scala b/hail/hail/src/is/hail/types/physical/PCanonicalString.scala
index ebce82c4403..4c425ff8f56 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalString.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalString.scala
@@ -12,7 +12,7 @@ case object PCanonicalStringOptional extends PCanonicalString(false)
 case object PCanonicalStringRequired extends PCanonicalString(true)
 
 class PCanonicalString(val required: Boolean) extends PString {
-  def _asIdent = "string"
+  override def _asIdent = "string"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PCString"
@@ -40,26 +40,26 @@ class PCanonicalString(val required: Boolean) extends PString {
 
   override def containsPointers: Boolean = true
 
-  def loadLength(boff: Long): Int =
+  override def loadLength(boff: Long): Int =
     this.binaryRepresentation.loadLength(boff)
 
-  def loadLength(boff: Code[Long]): Code[Int] =
+  override def loadLength(boff: Code[Long]): Code[Int] =
     this.binaryRepresentation.loadLength(boff)
 
-  def loadString(bAddress: Long): String =
+  override def loadString(bAddress: Long): String =
     new String(this.binaryRepresentation.loadBytes(bAddress))
 
-  def loadString(bAddress: Code[Long]): Code[String] =
+  override def loadString(bAddress: Code[Long]): Code[String] =
     Code.newInstance[String, Array[Byte]](this.binaryRepresentation.loadBytes(bAddress))
 
-  def allocateAndStoreString(region: Region, str: String): Long = {
+  override def allocateAndStoreString(region: Region, str: String): Long = {
     val byteRep = str.getBytes()
     val dstAddrss = this.binaryRepresentation.allocate(region, byteRep.length)
     this.binaryRepresentation.store(dstAddrss, byteRep)
     dstAddrss
   }
 
-  def allocateAndStoreString(cb: EmitCodeBuilder, region: Value[Region], str: Code[String])
+  override def allocateAndStoreString(cb: EmitCodeBuilder, region: Value[Region], str: Code[String])
     : Value[Long] = {
     val dstAddress = cb.newField[Long]("pcanonical_string_alloc_dst_address")
     val byteRep = cb.newField[Array[Byte]]("pcanonical_string_alloc_byte_rep")
@@ -86,15 +86,15 @@ class PCanonicalString(val required: Boolean) extends PString {
       deepCopy,
     )
 
-  def setRequired(required: Boolean): PCanonicalString =
+  override def setRequired(required: Boolean): PCanonicalString =
     if (required == this.required) this else PCanonicalString(required)
 
-  def sType: SStringPointer = SStringPointer(setRequired(false))
+  override def sType: SStringPointer = SStringPointer(setRequired(false))
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SStringPointerValue =
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SStringPointerValue =
     new SStringPointerValue(sType, cb.memoize(addr))
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     value.st match {
       case SStringPointer(t) if t.equalModuloRequired(this) && !deepCopy =>
@@ -104,7 +104,7 @@ class PCanonicalString(val required: Boolean) extends PString {
     }
   }
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -113,7 +113,8 @@ class PCanonicalString(val required: Boolean) extends PString {
   ): Unit =
     cb += Region.storeAddress(addr, store(cb, region, value, deepCopy))
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = binaryRepresentation.loadFromNested(addr)
+  override def loadFromNested(addr: Code[Long]): Code[Long] =
+    binaryRepresentation.loadFromNested(addr)
 
   override def unstagedLoadFromNested(addr: Long): Long =
     binaryRepresentation.unstagedLoadFromNested(addr)
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala b/hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala
index 455ba1daeb7..419de10a8d8 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalStruct.scala
@@ -1,10 +1,12 @@
 package is.hail.types.physical
 
 import is.hail.asm4s.{Code, Value}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{toRichIterable, toRichIterator}
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.virtual.{TStruct, Type}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.utils.implicits.toTruncatable
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -112,7 +114,7 @@ final case class PCanonicalStruct(fields: IndexedSeq[PField], required: Boolean
       ab += fields(i)
       i += 1
     }
-    val it = fieldsToInsert.toIterator
+    val it = fieldsToInsert.iterator
     while (it.hasNext) {
       val (name, typ) = it.next()
       if (fieldIdx.contains(name)) {
diff --git a/hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala b/hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala
index f824d96338c..006981c3f4d 100644
--- a/hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala
+++ b/hail/hail/src/is/hail/types/physical/PCanonicalTuple.scala
@@ -1,7 +1,7 @@
 package is.hail.types.physical
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.types.virtual.{TTuple, Type}
-import is.hail.utils._
 
 import scala.collection.compat._
 
@@ -20,7 +20,7 @@ final case class PCanonicalTuple(
     tf.index -> idx
   }.toMap
 
-  def setRequired(required: Boolean) =
+  override def setRequired(required: Boolean) =
     if (required == this.required) this else PCanonicalTuple(_types, required)
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
@@ -44,7 +44,7 @@ final case class PCanonicalTuple(
       this.required,
     )
 
-  def copiedType: PType = {
+  override def copiedType: PType = {
     val copiedTypes = types.map(_.copiedType)
     if (types.indices.forall(i => types(i).eq(copiedTypes(i))))
       this
diff --git a/hail/hail/src/is/hail/types/physical/PDict.scala b/hail/hail/src/is/hail/types/physical/PDict.scala
index c6cc0996ffd..2aba8dd609f 100644
--- a/hail/hail/src/is/hail/types/physical/PDict.scala
+++ b/hail/hail/src/is/hail/types/physical/PDict.scala
@@ -9,7 +9,7 @@ abstract class PDict extends PContainer {
   val keyType: PType
   val valueType: PType
 
-  def sType: SContainer
+  override def sType: SContainer
 
-  def elementType: PStruct
+  override def elementType: PStruct
 }
diff --git a/hail/hail/src/is/hail/types/physical/PFloat32.scala b/hail/hail/src/is/hail/types/physical/PFloat32.scala
index bc8c07558c3..21bc8c8dae2 100644
--- a/hail/hail/src/is/hail/types/physical/PFloat32.scala
+++ b/hail/hail/src/is/hail/types/physical/PFloat32.scala
@@ -16,13 +16,13 @@ class PFloat32(override val required: Boolean) extends PNumeric with PPrimitive
 
   override type NType = PFloat32
 
-  def _asIdent = "float32"
+  override def _asIdent = "float32"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PFloat32"
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int =
+    override def compare(o1: Long, o2: Long): Int =
       java.lang.Float.compare(Region.loadFloat(o1), Region.loadFloat(o2))
   }
 
@@ -38,7 +38,7 @@ class PFloat32(override val required: Boolean) extends PNumeric with PPrimitive
 
   override def sType: SType = SFloat32
 
-  def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
+  override def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
     cb.append(Region.storeFloat(addr, value.asFloat.value))
 
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SFloat32Value =
diff --git a/hail/hail/src/is/hail/types/physical/PFloat64.scala b/hail/hail/src/is/hail/types/physical/PFloat64.scala
index 04dd6186fcf..3e6454f1407 100644
--- a/hail/hail/src/is/hail/types/physical/PFloat64.scala
+++ b/hail/hail/src/is/hail/types/physical/PFloat64.scala
@@ -17,13 +17,13 @@ class PFloat64(override val required: Boolean) extends PNumeric with PPrimitive
 
   override type NType = PFloat64
 
-  def _asIdent = "float64"
+  override def _asIdent = "float64"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PFloat64"
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int =
+    override def compare(o1: Long, o2: Long): Int =
       java.lang.Double.compare(Region.loadDouble(o1), Region.loadDouble(o2))
   }
 
@@ -39,7 +39,7 @@ class PFloat64(override val required: Boolean) extends PNumeric with PPrimitive
 
   override def sType: SType = SFloat64
 
-  def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
+  override def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
     cb.append(Region.storeDouble(addr, value.asDouble.value))
 
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SFloat64Value =
diff --git a/hail/hail/src/is/hail/types/physical/PInt32.scala b/hail/hail/src/is/hail/types/physical/PInt32.scala
index 6ed69161613..de80955df40 100644
--- a/hail/hail/src/is/hail/types/physical/PInt32.scala
+++ b/hail/hail/src/is/hail/types/physical/PInt32.scala
@@ -13,7 +13,7 @@ case object PInt32Required extends PInt32(true)
 
 class PInt32(override val required: Boolean) extends PNumeric with PPrimitive {
   lazy val virtualType: TInt32.type = TInt32
-  def _asIdent = "int32"
+  override def _asIdent = "int32"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PInt32"
@@ -21,7 +21,7 @@ class PInt32(override val required: Boolean) extends PNumeric with PPrimitive {
   override type NType = PInt32
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int =
+    override def compare(o1: Long, o2: Long): Int =
       Integer.compare(Region.loadInt(o1), Region.loadInt(o2))
   }
 
@@ -37,7 +37,7 @@ class PInt32(override val required: Boolean) extends PNumeric with PPrimitive {
 
   override def sType: SType = SInt32
 
-  def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
+  override def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
     cb.append(Region.storeInt(addr, value.asInt.value))
 
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SInt32Value =
diff --git a/hail/hail/src/is/hail/types/physical/PInt64.scala b/hail/hail/src/is/hail/types/physical/PInt64.scala
index 7b90f36ba57..9020c6b6ba4 100644
--- a/hail/hail/src/is/hail/types/physical/PInt64.scala
+++ b/hail/hail/src/is/hail/types/physical/PInt64.scala
@@ -14,7 +14,7 @@ case object PInt64Required extends PInt64(true)
 class PInt64(override val required: Boolean) extends PNumeric with PPrimitive {
   lazy val virtualType: TInt64.type = TInt64
 
-  def _asIdent = "int64"
+  override def _asIdent = "int64"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PInt64"
@@ -22,7 +22,7 @@ class PInt64(override val required: Boolean) extends PNumeric with PPrimitive {
   override type NType = PInt64
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = new UnsafeOrdering {
-    def compare(o1: Long, o2: Long): Int =
+    override def compare(o1: Long, o2: Long): Int =
       java.lang.Long.compare(Region.loadLong(o1), Region.loadLong(o2))
   }
 
@@ -38,7 +38,7 @@ class PInt64(override val required: Boolean) extends PNumeric with PPrimitive {
 
   override def sType: SType = SInt64
 
-  def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
+  override def storePrimitiveAtAddress(cb: EmitCodeBuilder, addr: Code[Long], value: SValue): Unit =
     cb.append(Region.storeLong(addr, value.asLong.value))
 
   override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SInt64Value =
diff --git a/hail/hail/src/is/hail/types/physical/PInterval.scala b/hail/hail/src/is/hail/types/physical/PInterval.scala
index 0e9a7b1a927..401ad762861 100644
--- a/hail/hail/src/is/hail/types/physical/PInterval.scala
+++ b/hail/hail/src/is/hail/types/physical/PInterval.scala
@@ -15,7 +15,7 @@ abstract class PInterval extends PType {
     new UnsafeOrdering {
       private val pOrd = pointType.unsafeOrdering(sm)
 
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
         val sdef1 = startDefined(o1)
         if (sdef1 == startDefined(o2)) {
           val cmp = pOrd.compare(loadStart(o1), loadStart(o2))
@@ -47,7 +47,7 @@ abstract class PInterval extends PType {
     new UnsafeOrdering {
       private val pOrd = pointType.unsafeOrdering(sm)
 
-      def compare(o1: Long, o2: Long): Int = {
+      override def compare(o1: Long, o2: Long): Int = {
         val edef1 = endDefined(o1)
         if (edef1 == endDefined(o2)) {
           val cmp = pOrd.compare(loadEnd(o1), loadEnd(o2))
diff --git a/hail/hail/src/is/hail/types/physical/PPrimitive.scala b/hail/hail/src/is/hail/types/physical/PPrimitive.scala
index 5ad5b64a874..cc46361bc51 100644
--- a/hail/hail/src/is/hail/types/physical/PPrimitive.scala
+++ b/hail/hail/src/is/hail/types/physical/PPrimitive.scala
@@ -2,19 +2,17 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region}
 import is.hail.asm4s.{Code, _}
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.{EmitCodeBuilder, EmitMethodBuilder}
 import is.hail.types.physical.stypes.SValue
-import is.hail.utils._
 
 trait PPrimitive extends PType {
-  def byteSize: Long
-
   def _construct(mb: EmitMethodBuilder[_], region: Value[Region], pc: SValue): SValue = pc
 
   override def containsPointers: Boolean = false
 
-  def _copyFromAddress(
+  override def _copyFromAddress(
     sm: HailStateManager,
     region: Region,
     srcPType: PType,
@@ -30,7 +28,7 @@ trait PPrimitive extends PType {
     addr
   }
 
-  def unstagedStoreAtAddress(
+  override def unstagedStoreAtAddress(
     sm: HailStateManager,
     addr: Long,
     region: Region,
@@ -42,7 +40,7 @@ trait PPrimitive extends PType {
     Region.copyFrom(srcAddress, addr, byteSize)
   }
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] = {
     val newAddr = cb.memoize(region.allocate(alignment, byteSize))
     storeAtAddress(cb, newAddr, region, value, deepCopy)
@@ -67,7 +65,7 @@ trait PPrimitive extends PType {
     addr
   }
 
-  def setRequired(required: Boolean): PPrimitive = {
+  override def setRequired(required: Boolean): PPrimitive = {
     if (required == this.required)
       this
     else
@@ -80,7 +78,7 @@ trait PPrimitive extends PType {
       }
   }
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = addr
+  override def loadFromNested(addr: Code[Long]): Code[Long] = addr
 
   override def unstagedLoadFromNested(addr: Long): Long = addr
 
diff --git a/hail/hail/src/is/hail/types/physical/PStruct.scala b/hail/hail/src/is/hail/types/physical/PStruct.scala
index 23d7eb4d8f9..0422aca8171 100644
--- a/hail/hail/src/is/hail/types/physical/PStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/PStruct.scala
@@ -2,7 +2,7 @@ package is.hail.types.physical
 
 import is.hail.asm4s.{Code, Value}
 import is.hail.expr.ir.EmitCodeBuilder
-import is.hail.types.physical.stypes.interfaces.{SBaseStruct, SBaseStructValue}
+import is.hail.types.physical.stypes.interfaces.SBaseStruct
 import is.hail.types.virtual.{Field, TStruct}
 
 import scala.collection.compat._
@@ -35,7 +35,7 @@ trait PStruct extends PBaseStruct {
 
   def rename(m: Map[String, String]): PStruct
 
-  def identBase: String = "struct"
+  override def identBase: String = "struct"
 
   final def selectFields(names: Seq[String]): PCanonicalStruct =
     PCanonicalStruct(required, names.map(f => f -> field(f).typ): _*)
@@ -61,6 +61,4 @@ trait PStruct extends PBaseStruct {
   def setFieldMissing(cb: EmitCodeBuilder, offset: Code[Long], fieldName: String): Unit
 
   def insertFields(fieldsToInsert: IterableOnce[(String, PType)]): PStruct
-
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBaseStructValue
 }
diff --git a/hail/hail/src/is/hail/types/physical/PSubsetStruct.scala b/hail/hail/src/is/hail/types/physical/PSubsetStruct.scala
index 14695382838..eeffba37359 100644
--- a/hail/hail/src/is/hail/types/physical/PSubsetStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/PSubsetStruct.scala
@@ -3,6 +3,7 @@ package is.hail.types.physical
 import is.hail.annotations.{Annotation, Region}
 import is.hail.asm4s.{Code, Value}
 import is.hail.backend.HailStateManager
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.SValue
 import is.hail.types.physical.stypes.concrete.SStructView
@@ -79,7 +80,7 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
   override def fieldOffset(structAddress: Code[Long], fieldIdx: Int): Code[Long] =
     ps.fieldOffset(structAddress, idxMap(fieldIdx))
 
-  def loadField(structAddress: Code[Long], fieldName: String): Code[Long] =
+  override def loadField(structAddress: Code[Long], fieldName: String): Code[Long] =
     ps.loadField(structAddress, fieldName)
 
   override def loadField(structAddress: Long, fieldIdx: Int): Long =
@@ -104,7 +105,7 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
   override def setFieldPresent(cb: EmitCodeBuilder, structAddress: Code[Long], fieldIdx: Int)
     : Unit = ???
 
-  def insertFields(fieldsToInsert: IterableOnce[(String, PType)]): PSubsetStruct = ???
+  override def insertFields(fieldsToInsert: IterableOnce[(String, PType)]): PSubsetStruct = ???
 
   override def initialize(structAddress: Long, setMissing: Boolean): Unit =
     ps.initialize(structAddress, setMissing)
@@ -113,10 +114,10 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
     : Unit =
     ps.stagedInitialize(cb, structAddress, setMissing)
 
-  def allocate(region: Region): Long =
+  override def allocate(region: Region): Long =
     ps.allocate(region)
 
-  def allocate(region: Code[Region]): Code[Long] =
+  override def allocate(region: Code[Region]): Code[Long] =
     ps.allocate(region)
 
   override def setRequired(required: Boolean): PType =
@@ -140,14 +141,14 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
   ): Long =
     throw new UnsupportedOperationException
 
-  def sType: SBaseStruct =
+  override def sType: SBaseStruct =
     SStructView.subset(_fieldNames, ps.sType)
 
-  def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
+  override def store(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
     : Value[Long] =
     throw new UnsupportedOperationException
 
-  def storeAtAddress(
+  override def storeAtAddress(
     cb: EmitCodeBuilder,
     addr: Code[Long],
     region: Value[Region],
@@ -156,10 +157,10 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
   ): Unit =
     throw new UnsupportedOperationException
 
-  def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBaseStructValue =
+  override def loadCheapSCode(cb: EmitCodeBuilder, addr: Code[Long]): SBaseStructValue =
     throw new UnsupportedOperationException
 
-  def unstagedStoreAtAddress(
+  override def unstagedStoreAtAddress(
     sm: HailStateManager,
     addr: Long,
     region: Region,
@@ -169,7 +170,7 @@ final case class PSubsetStruct(ps: PStruct, _fieldNames: IndexedSeq[String])
   ): Unit =
     throw new UnsupportedOperationException
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = addr
+  override def loadFromNested(addr: Code[Long]): Code[Long] = addr
 
   override def unstagedLoadFromNested(addr: Long): Long = addr
 
diff --git a/hail/hail/src/is/hail/types/physical/PTuple.scala b/hail/hail/src/is/hail/types/physical/PTuple.scala
index 58310f736fa..9e8fa2c19e2 100644
--- a/hail/hail/src/is/hail/types/physical/PTuple.scala
+++ b/hail/hail/src/is/hail/types/physical/PTuple.scala
@@ -16,5 +16,5 @@ trait PTuple extends PBaseStruct {
 
   lazy val nFields: Int = fields.size
 
-  def identBase: String = "tuple"
+  override def identBase: String = "tuple"
 }
diff --git a/hail/hail/src/is/hail/types/physical/PType.scala b/hail/hail/src/is/hail/types/physical/PType.scala
index 25c58a0f9bd..d0776d3ff7d 100644
--- a/hail/hail/src/is/hail/types/physical/PType.scala
+++ b/hail/hail/src/is/hail/types/physical/PType.scala
@@ -3,6 +3,7 @@ package is.hail.types.physical
 import is.hail.annotations._
 import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.{BooleanArrayBuilder, FastSeq, IntArrayBuilder}
 import is.hail.expr.ir._
 import is.hail.types.{tcoerce, Requiredness}
 import is.hail.types.physical.stypes.{SType, SValue}
diff --git a/hail/hail/src/is/hail/types/physical/PUnrealizable.scala b/hail/hail/src/is/hail/types/physical/PUnrealizable.scala
index 0219ea824af..f484c7cc483 100644
--- a/hail/hail/src/is/hail/types/physical/PUnrealizable.scala
+++ b/hail/hail/src/is/hail/types/physical/PUnrealizable.scala
@@ -14,7 +14,7 @@ trait PUnrealizable extends PType {
 
   override def alignment: Long = unsupported
 
-  protected[physical] def _copyFromAddress(
+  override protected[physical] def _copyFromAddress(
     sm: HailStateManager,
     region: Region,
     srcPType: PType,
@@ -32,7 +32,7 @@ trait PUnrealizable extends PType {
   ): Long =
     unsupported
 
-  def unstagedStoreAtAddress(
+  override def unstagedStoreAtAddress(
     sm: HailStateManager,
     addr: Long,
     region: Region,
diff --git a/hail/hail/src/is/hail/types/physical/PVoid.scala b/hail/hail/src/is/hail/types/physical/PVoid.scala
index 0200863f9c0..d74ce38952b 100644
--- a/hail/hail/src/is/hail/types/physical/PVoid.scala
+++ b/hail/hail/src/is/hail/types/physical/PVoid.scala
@@ -11,21 +11,21 @@ case object PVoid extends PType with PUnrealizable {
 
   override def sType: SType = SVoid
 
-  def virtualType: Type = TVoid
+  override def virtualType: Type = TVoid
 
   override val required = true
 
-  def _asIdent = "void"
+  override def _asIdent = "void"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     sb ++= "PVoid"
 
-  def setRequired(required: Boolean) = PVoid
+  override def setRequired(required: Boolean) = PVoid
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering =
     throw new NotImplementedError()
 
-  def loadFromNested(addr: Code[Long]): Code[Long] = throw new NotImplementedError()
+  override def loadFromNested(addr: Code[Long]): Code[Long] = throw new NotImplementedError()
 
   override def unstagedLoadFromNested(addr: Long): Long = throw new NotImplementedError()
 }
diff --git a/hail/hail/src/is/hail/types/physical/StoredSTypePType.scala b/hail/hail/src/is/hail/types/physical/StoredSTypePType.scala
index 8e47c4ae588..227f19db91c 100644
--- a/hail/hail/src/is/hail/types/physical/StoredSTypePType.scala
+++ b/hail/hail/src/is/hail/types/physical/StoredSTypePType.scala
@@ -2,6 +2,7 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region, UnsafeOrdering}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
 import is.hail.backend.HailStateManager
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.stypes.{SType, SValue}
@@ -117,7 +118,7 @@ case class StoredSTypePType(sType: SType, required: Boolean) extends PType {
 
   override def deepRename(t: Type): PType = StoredSTypePType(sType.castRename(t), required)
 
-  def byteSize: Long = ct.byteSize
+  override def byteSize: Long = ct.byteSize
 
   override def alignment: Long = ct.alignment
 
@@ -137,12 +138,13 @@ case class StoredSTypePType(sType: SType, required: Boolean) extends PType {
 
   override def unsafeOrdering(sm: HailStateManager): UnsafeOrdering = unsupportedCanonicalMethod
 
-  def unstagedLoadFromNested(addr: Long): Long = unsupportedCanonicalMethod
+  override def unstagedLoadFromNested(addr: Long): Long = unsupportedCanonicalMethod
 
-  def unstagedStoreJavaObject(sm: HailStateManager, annotation: Annotation, region: Region): Long =
+  override def unstagedStoreJavaObject(sm: HailStateManager, annotation: Annotation, region: Region)
+    : Long =
     unsupportedCanonicalMethod
 
-  def unstagedStoreJavaObjectAtAddress(
+  override def unstagedStoreJavaObjectAtAddress(
     sm: HailStateManager,
     addr: Long,
     annotation: Annotation,
diff --git a/hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala b/hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala
index 334929a0b86..6035c35fae4 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/SingleCodeSCode.scala
@@ -46,72 +46,97 @@ sealed trait SingleCodeType {
 }
 
 case object Int32SingleCodeType extends SingleCodeType {
-  def ti: TypeInfo[_] = IntInfo
+  override def ti: TypeInfo[_] = IntInfo
 
   override def loadedSType: SType = SInt32
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue = new SInt32Value(coerce[Int](c))
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+    new SInt32Value(coerce[Int](c))
 
-  def virtualType: Type = TInt32
+  override def virtualType: Type = TInt32
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pc.asInt.value)
 }
 
 case object Int64SingleCodeType extends SingleCodeType {
-  def ti: TypeInfo[_] = LongInfo
+  override def ti: TypeInfo[_] = LongInfo
 
   override def loadedSType: SType = SInt64
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue = new SInt64Value(coerce[Long](c))
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+    new SInt64Value(coerce[Long](c))
 
-  def virtualType: Type = TInt64
+  override def virtualType: Type = TInt64
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pc.asLong.value)
 }
 
 case object Float32SingleCodeType extends SingleCodeType {
-  def ti: TypeInfo[_] = FloatInfo
+  override def ti: TypeInfo[_] = FloatInfo
 
   override def loadedSType: SType = SFloat32
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue = new SFloat32Value(coerce[Float](c))
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+    new SFloat32Value(coerce[Float](c))
 
-  def virtualType: Type = TFloat32
+  override def virtualType: Type = TFloat32
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pc.asFloat.value)
 }
 
 case object Float64SingleCodeType extends SingleCodeType {
-  def ti: TypeInfo[_] = DoubleInfo
+  override def ti: TypeInfo[_] = DoubleInfo
 
   override def loadedSType: SType = SFloat64
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue = new SFloat64Value(coerce[Double](c))
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+    new SFloat64Value(coerce[Double](c))
 
-  def virtualType: Type = TFloat64
+  override def virtualType: Type = TFloat64
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pc.asDouble.value)
 }
 
 case object BooleanSingleCodeType extends SingleCodeType {
-  def ti: TypeInfo[_] = BooleanInfo
+  override def ti: TypeInfo[_] = BooleanInfo
 
   override def loadedSType: SType = SBoolean
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue = new SBooleanValue(coerce[Boolean](c))
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+    new SBooleanValue(coerce[Boolean](c))
 
-  def virtualType: Type = TBoolean
+  override def virtualType: Type = TBoolean
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pc.asBoolean.value)
 }
 
@@ -124,33 +149,41 @@ case class StreamSingleCodeType(
 
   override def loadedSType: SType = SStream(EmitType(eltType.sType, true))
 
-  def virtualType: Type = TStream(eltType.virtualType)
+  override def virtualType: Type = TStream(eltType.virtualType)
 
-  def ti: TypeInfo[_] = classInfo[NoBoxLongIterator]
+  override def ti: TypeInfo[_] = classInfo[NoBoxLongIterator]
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
     new SStreamConcrete(
       SStreamIteratorLong(eltRequired, eltType, requiresMemoryManagementPerElement),
       coerce[NoBoxLongIterator](c),
     )
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     throw new UnsupportedOperationException
 }
 
 case class PTypeReferenceSingleCodeType(pt: PType) extends SingleCodeType {
-  def ti: TypeInfo[_] = LongInfo
+  override def ti: TypeInfo[_] = LongInfo
 
   override def loadedSType: SType = pt.sType
 
-  def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
+  override def loadToSValue(cb: EmitCodeBuilder, c: Value[_]): SValue =
     cb.memoizeField(pt.loadCheapSCode(cb, coerce[Long](c)), "PTypeReferenceSingleCodeType")
 
-  def virtualType: Type = pt.virtualType
+  override def virtualType: Type = pt.virtualType
 
-  def coerceSCode(cb: EmitCodeBuilder, pc: SValue, region: Value[Region], deepCopy: Boolean)
-    : SingleCodeSCode =
+  override def coerceSCode(
+    cb: EmitCodeBuilder,
+    pc: SValue,
+    region: Value[Region],
+    deepCopy: Boolean,
+  ): SingleCodeSCode =
     SingleCodeSCode(this, pt.store(cb, region, pc, deepCopy = deepCopy))
 }
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
index 1fbcf2f8947..2a3fadf5e8d 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBaseStructPointer.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical.{PBaseStruct, PType}
 import is.hail.types.physical.stypes.{EmitType, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SBaseStruct, SBaseStructSettable, SBaseStructValue}
 import is.hail.types.virtual.{TBaseStruct, Type}
-import is.hail.utils.FastSeq
 
 final case class SBaseStructPointer(pType: PBaseStruct) extends SBaseStruct {
   require(!pType.required)
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
index 5bf3ab23250..7476fd3e9ec 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SBinaryPointer.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PBinary, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SBinary, SBinaryValue}
 import is.hail.types.virtual.Type
-import is.hail.utils._
 
 final case class SBinaryPointer(pType: PBinary) extends SBinary {
   require(!pType.required)
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
index 5f0266619d9..82d38963279 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalCall.scala
@@ -2,18 +2,22 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCall, PCanonicalCall, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SCall, SCallValue, SIndexableValue}
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual.{TCall, Type}
-import is.hail.utils._
 import is.hail.variant._
 
 case object SCanonicalCall extends SCall {
-  def _coerceOrCopy(cb: EmitCodeBuilder, region: Value[Region], value: SValue, deepCopy: Boolean)
-    : SValue =
+  override def _coerceOrCopy(
+    cb: EmitCodeBuilder,
+    region: Value[Region],
+    value: SValue,
+    deepCopy: Boolean,
+  ): SValue =
     value.st match {
       case SCanonicalCall => value
     }
@@ -22,25 +26,25 @@ case object SCanonicalCall extends SCall {
 
   override def castRename(t: Type): SType = this
 
-  def settableTupleTypes(): IndexedSeq[TypeInfo[_]] = FastSeq(IntInfo)
+  override def settableTupleTypes(): IndexedSeq[TypeInfo[_]] = FastSeq(IntInfo)
 
-  def fromSettables(settables: IndexedSeq[Settable[_]]): SCanonicalCallSettable = {
+  override def fromSettables(settables: IndexedSeq[Settable[_]]): SCanonicalCallSettable = {
     val IndexedSeq(call: Settable[Int @unchecked]) = settables
     assert(call.ti == IntInfo)
     new SCanonicalCallSettable(call)
   }
 
-  def fromValues(values: IndexedSeq[Value[_]]): SCanonicalCallValue = {
+  override def fromValues(values: IndexedSeq[Value[_]]): SCanonicalCallValue = {
     val IndexedSeq(call: Value[Int @unchecked]) = values
     assert(call.ti == IntInfo)
     new SCanonicalCallValue(call)
   }
 
-  def storageType(): PType = PCanonicalCall(false)
+  override def storageType(): PType = PCanonicalCall(false)
 
-  def copiedType: SType = this
+  override def copiedType: SType = this
 
-  def containsPointers: Boolean = false
+  override def containsPointers: Boolean = false
 
   def constructFromIntRepr(cb: EmitCodeBuilder, c: Code[Int]): SCanonicalCallValue =
     new SCanonicalCallValue(cb.memoize(c))
@@ -59,7 +63,7 @@ class SCanonicalCallValue(val call: Value[Int]) extends SCallValue {
     new SCanonicalCallValue(repr)
   }
 
-  def containsAllele(cb: EmitCodeBuilder, allele: Value[Int]): Value[Boolean] =
+  override def containsAllele(cb: EmitCodeBuilder, allele: Value[Int]): Value[Boolean] =
     cb.memoize[Boolean](
       Code.invokeScalaObject2[Int, Int, Boolean](
         Call.getClass,
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
index 05922aa2b22..0896808fb4e 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SCanonicalLocusPointer.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCanonicalLocus, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.Type
-import is.hail.utils.FastSeq
 
 final case class SCanonicalLocusPointer(pType: PCanonicalLocus) extends SLocus {
   require(!pType.required)
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
index d3b74359cf2..06f1abbcce8 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIndexablePointer.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces.{SContainer, SIndexableValue}
 import is.hail.types.virtual.Type
-import is.hail.utils.FastSeq
 
 final case class SIndexablePointer(pType: PContainer) extends SContainer {
   require(!pType.required)
@@ -134,9 +134,9 @@ final class SIndexablePointerSettable(
   override val length: Settable[Int],
   override val elementsAddress: Settable[Long],
 ) extends SIndexablePointerValue(st, a, length, elementsAddress) with SSettable {
-  def settableTuple(): IndexedSeq[Settable[_]] = FastSeq(a, length, elementsAddress)
+  override def settableTuple(): IndexedSeq[Settable[_]] = FastSeq(a, length, elementsAddress)
 
-  def store(cb: EmitCodeBuilder, v: SValue): Unit = v match {
+  override def store(cb: EmitCodeBuilder, v: SValue): Unit = v match {
     case v: SIndexablePointerValue =>
       cb.assign(a, v.a)
       cb.assign(length, v.length)
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
index 67d7b15aebe..02a9c5ad5b9 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SIntervalPointer.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{BooleanInfo, LongInfo, Settable, SettableBuilder, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical.{PInterval, PType}
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces.{SInterval, SIntervalValue}
 import is.hail.types.virtual.Type
-import is.hail.utils.FastSeq
 
 final case class SIntervalPointer(pType: PInterval) extends SInterval {
   require(!pType.required)
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala
index 0f49d96c6b9..fec0e5329d2 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaArray.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, IEmitCode}
 import is.hail.types.physical.{PCanonicalArray, PCanonicalString, PString, PType}
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces.{SContainer, SIndexableValue, SStringValue}
 import is.hail.types.virtual.{TArray, TString, Type}
-import is.hail.utils.FastSeq
 
 object SJavaArrayHelpers {
   def hasNulls(a: Array[String]): Boolean = {
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
index c0d422f3b22..bc2ab97b435 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaBytes.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCanonicalBinary, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SBinary, SBinaryValue}
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 case object SJavaBytes extends SBinary {
   override val virtualType: TBinary.type = TBinary
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala
index 5bf9a8c0c52..ddccee29417 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SJavaString.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCanonicalString, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual.{TString, Type}
-import is.hail.utils.FastSeq
 
 case object SJavaString extends SString {
   override val virtualType: TString.type = TString
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
index b356a5454b0..abc7737d234 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArrayPointer.scala
@@ -2,12 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PCanonicalNDArray, PType}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual.Type
-import is.hail.utils.{toRichIterable, FastSeq}
 
 import scala.collection.compat._
 
@@ -153,10 +154,10 @@ final class SNDArrayPointerSettable(
   override val firstDataAddress: Settable[Long],
 ) extends SNDArrayPointerValue(st, a, shape.map(SizeValueDyn.apply), strides, firstDataAddress)
     with SNDArraySettable {
-  def settableTuple(): IndexedSeq[Settable[_]] =
+  override def settableTuple(): IndexedSeq[Settable[_]] =
     FastSeq(a) ++ shape ++ strides ++ FastSeq(firstDataAddress)
 
-  def store(cb: EmitCodeBuilder, v: SValue): Unit = v match {
+  override def store(cb: EmitCodeBuilder, v: SValue): Unit = v match {
     case v: SNDArrayPointerValue =>
       cb.assign(a, v.a)
       shape.lazyZip(v.shapes).foreach(cb.assign(_, _))
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
index 1a3d37d616f..5f5c2b3c2f7 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SNDArraySlice.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{EmitCodeBuilder, EmitValue}
 import is.hail.types.physical.{PCanonicalNDArray, PType}
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.SInt64
 import is.hail.types.virtual.{TNDArray, Type}
-import is.hail.utils.toRichIterable
 
 import scala.collection.compat._
 
@@ -86,7 +86,8 @@ class SNDArraySliceValue(
   override def loadElement(indices: IndexedSeq[Value[Long]], cb: EmitCodeBuilder): SValue =
     pt.elementType.loadCheapSCode(cb, loadElementAddress(indices, cb))
 
-  def coerceToShape(cb: EmitCodeBuilder, otherShape: IndexedSeq[SizeValue]): SNDArrayValue = {
+  override def coerceToShape(cb: EmitCodeBuilder, otherShape: IndexedSeq[SizeValue])
+    : SNDArrayValue = {
     cb.if_(!hasShape(cb, otherShape), cb._fatal("incompatible shapes"))
     new SNDArraySliceValue(st, otherShape, strides, firstDataAddress)
   }
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala
index b65926a3e29..c67ec129d52 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SRNGState.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, Threefry, ThreefryRandomEngine}
 import is.hail.types.{RPrimitive, TypeWithRequiredness}
 import is.hail.types.physical.{PType, StoredSTypePType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual.{TRNGState, Type}
-import is.hail.utils.FastSeq
 
 import scala.collection.compat._
 
@@ -21,7 +21,7 @@ final case class SRNGStateStaticInfo(
 }
 
 final case class SRNGState(staticInfo: Option[SRNGStateStaticInfo]) extends SType {
-  def virtualType: Type = TRNGState
+  override def virtualType: Type = TRNGState
 
   override protected[stypes] def _typeWithRequiredness: TypeWithRequiredness =
     RPrimitive()
@@ -130,7 +130,7 @@ class SCanonicalRNGStateValue(
   override def sizeToStoreInBytes(cb: EmitCodeBuilder): SInt64Value =
     new SInt64Value(4 * 8 + 4 * 8 + 4 + 4 + 4)
 
-  def splitStatic(cb: EmitCodeBuilder, idx: Long): SCanonicalRNGStateValue = {
+  override def splitStatic(cb: EmitCodeBuilder, idx: Long): SCanonicalRNGStateValue = {
     cb.if_(hasStaticSplit, cb._fatal("RNGState received two static splits"))
     val x = Array.ofDim[Long](4)
     x(0) = cb.emb.ctx.rngNonce
@@ -149,7 +149,7 @@ class SCanonicalRNGStateValue(
     )
   }
 
-  def splitDyn(cb: EmitCodeBuilder, idx: Value[Long]): SCanonicalRNGStateValue = {
+  override def splitDyn(cb: EmitCodeBuilder, idx: Value[Long]): SCanonicalRNGStateValue = {
     val newRunningSum =
       Array.tabulate[Settable[Long]](4)(i => cb.newLocal[Long](s"splitDyn_x$i", runningSum(i)))
     val newLastDynBlock =
@@ -180,7 +180,7 @@ class SCanonicalRNGStateValue(
       hasStaticSplit, newNumDynBlocks)
   }
 
-  def rand(cb: EmitCodeBuilder): IndexedSeq[Value[Long]] = {
+  override def rand(cb: EmitCodeBuilder): IndexedSeq[Value[Long]] = {
     cb.if_(!hasStaticSplit, cb._fatal("RNGState never received static split"))
     val x = Array.tabulate[Settable[Long]](4)(i => cb.newLocal[Long](s"rand_x$i", runningSum(i)))
     val key = Threefry.defaultKey
@@ -204,7 +204,7 @@ class SCanonicalRNGStateValue(
     x
   }
 
-  def copyIntoEngine(cb: EmitCodeBuilder, tf: Value[ThreefryRandomEngine]): Unit = {
+  override def copyIntoEngine(cb: EmitCodeBuilder, tf: Value[ThreefryRandomEngine]): Unit = {
     cb.if_(!hasStaticSplit, cb._fatal("RNGState never received static split"))
     val x = Array.tabulate[Settable[Long]](4)(i => cb.newLocal[Long](s"cie_x$i", runningSum(i)))
     val finalTweak =
@@ -282,7 +282,7 @@ class SRNGStateStaticSizeValue(
   override def sizeToStoreInBytes(cb: EmitCodeBuilder): SInt64Value =
     new SInt64Value(4 * 8 + staticInfo.numWordsInLastBlock * 8)
 
-  def splitStatic(cb: EmitCodeBuilder, idx: Long): SRNGStateStaticSizeValue = {
+  override def splitStatic(cb: EmitCodeBuilder, idx: Long): SRNGStateStaticSizeValue = {
     assert(!staticInfo.hasStaticSplit)
     val x = Array.ofDim[Long](4)
     x(0) = cb.emb.ctx.rngNonce
@@ -302,7 +302,7 @@ class SRNGStateStaticSizeValue(
     )
   }
 
-  def splitDyn(cb: EmitCodeBuilder, idx: Value[Long]): SRNGStateStaticSizeValue = {
+  override def splitDyn(cb: EmitCodeBuilder, idx: Value[Long]): SRNGStateStaticSizeValue = {
     if (staticInfo.numWordsInLastBlock < 4) {
       return new SRNGStateStaticSizeValue(
         st = SRNGState(Some(SRNGStateStaticInfo(
@@ -331,7 +331,7 @@ class SRNGStateStaticSizeValue(
     )
   }
 
-  def rand(cb: EmitCodeBuilder): IndexedSeq[Value[Long]] = {
+  override def rand(cb: EmitCodeBuilder): IndexedSeq[Value[Long]] = {
     assert(staticInfo.hasStaticSplit)
     val x = Array.tabulate[Settable[Long]](4)(i => cb.newLocal[Long](s"rand_x$i", runningSum(i)))
     val key = Threefry.defaultKey
@@ -346,7 +346,7 @@ class SRNGStateStaticSizeValue(
     x
   }
 
-  def copyIntoEngine(cb: EmitCodeBuilder, tf: Value[ThreefryRandomEngine]): Unit = {
+  override def copyIntoEngine(cb: EmitCodeBuilder, tf: Value[ThreefryRandomEngine]): Unit = {
     val x = Array.tabulate[Settable[Long]](4)(i => cb.newLocal[Long](s"cie_x$i", runningSum(i)))
     for (i <- lastDynBlock.indices) cb.assign(x(i), x(i) ^ lastDynBlock(i))
     val finalTweak = if (staticInfo.numWordsInLastBlock < 4) {
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala
index 0f90fa5c159..429c668d25d 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackInterval.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, EmitSettable, EmitValue, IEmitCode}
 import is.hail.types.physical.PType
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces.{SInterval, SIntervalValue}
 import is.hail.types.virtual.{TInterval, Type}
-import is.hail.utils.FastSeq
 
 object SStackInterval {
   def construct(
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala
index 16adcf81d14..aee582e1237 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStackStruct.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder, EmitSettable, EmitValue, IEmitCode}
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.{EmitType, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SBaseStruct, SBaseStructSettable, SBaseStructValue}
 import is.hail.types.virtual.{TBaseStruct, TStruct, TTuple, Type}
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala
index 82f27e81aa1..84ad8fd83dc 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStringPointer.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, LongInfo, Settable, SettableBuilder, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PString, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.physical.stypes.interfaces.{SString, SStringValue}
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual.Type
-import is.hail.utils.FastSeq
 
 final case class SStringPointer(pType: PString) extends SString {
   require(!pType.required)
@@ -58,13 +58,13 @@ class SStringPointerValue(val st: SStringPointer, val a: Value[Long]) extends SS
   def binaryRepr: SBinaryPointerValue =
     new SBinaryPointerValue(SBinaryPointer(pt.binaryRepresentation), a)
 
-  def loadLength(cb: EmitCodeBuilder): Value[Int] =
+  override def loadLength(cb: EmitCodeBuilder): Value[Int] =
     cb.memoize(pt.loadLength(a))
 
-  def loadString(cb: EmitCodeBuilder): Value[String] =
+  override def loadString(cb: EmitCodeBuilder): Value[String] =
     cb.memoize(pt.loadString(a))
 
-  def toBytes(cb: EmitCodeBuilder): SBinaryPointerValue =
+  override def toBytes(cb: EmitCodeBuilder): SBinaryPointerValue =
     binaryRepr
 
   override def sizeToStoreInBytes(cb: EmitCodeBuilder): SInt64Value =
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala
index 7a970e49c8b..aec31c20010 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SStructView.scala
@@ -106,7 +106,7 @@ final class SStructView(
       ct
     }
 
-  def storageType(): PType = {
+  override def storageType(): PType = {
     val pt = PCanonicalStruct(
       required = false,
       args = rename.fieldNames.zip(fieldEmitTypes.map(_.copiedType.storageType)): _*,
diff --git a/hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala b/hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala
index a584abc8195..13e4e8aba21 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/concrete/SUnreachable.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.concrete
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, EmitValue, IEmitCode}
 import is.hail.types.physical.{PCanonicalNDArray, PNDArray, PType}
 import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 object SUnreachable {
   def fromVirtualType(t: Type): SType = {
@@ -169,7 +169,8 @@ case object SUnreachableCall extends SUnreachable with SCall {
 class SUnreachableCallValue extends SUnreachableValue with SCallValue {
   override def unphase(cb: EmitCodeBuilder): SCallValue = this
 
-  def containsAllele(cb: EmitCodeBuilder, allele: Value[Int]): Value[Boolean] = const(false)
+  override def containsAllele(cb: EmitCodeBuilder, allele: Value[Int]): Value[Boolean] =
+    const(false)
 
   override def forEachAllele(cb: EmitCodeBuilder)(alleleCode: Value[Int] => Unit): Unit = {}
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
index 9f3cc00b0bd..ba891811714 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SBaseStruct.scala
@@ -2,6 +2,7 @@ package is.hail.types.physical.stypes.interfaces
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder, EmitValue, IEmitCode}
 import is.hail.types.{RStruct, RTuple, TypeWithRequiredness}
 import is.hail.types.physical.PCanonicalStruct
@@ -9,7 +10,6 @@ import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.concrete._
 import is.hail.types.physical.stypes.primitives.{SInt32Value, SInt64Value}
 import is.hail.types.virtual.{TBaseStruct, TStruct, TTuple}
-import is.hail.utils._
 
 object SBaseStruct {
   def merge(cb: EmitCodeBuilder, s1: SBaseStructValue, s2: SBaseStructValue): SBaseStructValue = {
@@ -33,7 +33,7 @@ object SBaseStruct {
 }
 
 trait SBaseStruct extends SType {
-  def virtualType: TBaseStruct
+  override def virtualType: TBaseStruct
 
   def size: Int
 
@@ -42,7 +42,7 @@ trait SBaseStruct extends SType {
 
   def fieldIdx(fieldName: String): Int
 
-  def _typeWithRequiredness: TypeWithRequiredness = {
+  override def _typeWithRequiredness: TypeWithRequiredness = {
     virtualType match {
       case ts: TStruct => RStruct.fromNamesAndTypes(ts.fieldNames.zip(fieldEmitTypes).map {
           case (name, et) => (name, et.typeWithRequiredness.r)
@@ -57,7 +57,7 @@ trait SBaseStruct extends SType {
 trait SBaseStructSettable extends SBaseStructValue with SSettable
 
 trait SBaseStructValue extends SValue {
-  def st: SBaseStruct
+  override def st: SBaseStruct
 
   def isFieldMissing(cb: EmitCodeBuilder, fieldIdx: Int): Value[Boolean]
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala
index 61de1ee8f14..2c61d1ff483 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SContainer.scala
@@ -17,7 +17,7 @@ trait SContainer extends SType {
 }
 
 trait SIndexableValue extends SValue {
-  def st: SContainer
+  override def st: SContainer
 
   def loadLength: Value[Int]
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala
index fb67fbe0827..7711311a6c5 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SInterval.scala
@@ -18,7 +18,7 @@ trait SInterval extends SType {
 }
 
 trait SIntervalValue extends SValue {
-  def st: SInterval
+  override def st: SInterval
 
   def includesStart: Value[Boolean]
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala
index ec5ccf2ac7c..9b672906218 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SNDArray.scala
@@ -2,6 +2,9 @@ package is.hail.types.physical.stypes.interfaces
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.linalg.{BLAS, LAPACK}
 import is.hail.types.{RNDArray, TypeWithRequiredness}
@@ -10,7 +13,6 @@ import is.hail.types.physical.stypes.{EmitType, SSettable, SType, SValue}
 import is.hail.types.physical.stypes.concrete.{SNDArraySlice, SNDArraySliceValue}
 import is.hail.types.physical.stypes.primitives.SInt64Value
 import is.hail.types.virtual.TInt32
-import is.hail.utils.{toRichIterable, valueToRichCodeRegion, FastSeq}
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -1243,7 +1245,7 @@ object SizeValueStatic {
 }
 
 final class SizeValueDyn(val v: Value[Long]) extends SizeValue {
-  def get: Code[Long] = v.get
+  override def get: Code[Long] = v.get
 
   override def equals(other: Any): Boolean = other match {
     case SizeValueDyn(v2) => v eq v2
@@ -1252,7 +1254,7 @@ final class SizeValueDyn(val v: Value[Long]) extends SizeValue {
 }
 
 final class SizeValueStatic(val v: Long) extends SizeValue {
-  def get: Code[Long] = const(v)
+  override def get: Code[Long] = const(v)
 
   override def equals(other: Any): Boolean = other match {
     case SizeValueStatic(v2) => v == v2
@@ -1261,7 +1263,7 @@ final class SizeValueStatic(val v: Long) extends SizeValue {
 }
 
 trait SNDArrayValue extends SValue {
-  def st: SNDArray
+  override def st: SNDArray
 
   def pt: PNDArray
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala
index ac27349918b..c8aeedb7b5c 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SStream.scala
@@ -2,13 +2,13 @@ package is.hail.types.physical.stypes.interfaces
 
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCode, EmitCodeBuilder, EmitMethodBuilder, IEmitCode}
 import is.hail.expr.ir.streams.StreamProducer
 import is.hail.types.{RIterable, TypeWithRequiredness}
 import is.hail.types.physical.PType
 import is.hail.types.physical.stypes._
 import is.hail.types.virtual.{TStream, Type}
-import is.hail.utils.FastSeq
 
 trait MissingnessAsMethod {
   def isMissing: Boolean
@@ -95,7 +95,7 @@ object SStreamValue {
 }
 
 trait SStreamValue extends SUnrealizableValue {
-  def st: SStream
+  override def st: SStream
 
   def getProducer(mb: EmitMethodBuilder[_]): StreamProducer
 
@@ -160,7 +160,7 @@ case class SStreamControlFlow(st: SimpleSStream, producer: StreamProducer) exten
     producer
   }
 
-  def valueTuple: IndexedSeq[Value[_]] = throw new NotImplementedError()
+  override def valueTuple: IndexedSeq[Value[_]] = throw new NotImplementedError()
 
   override def defineUnusedLabels(mb: EmitMethodBuilder[_]): Unit = {
     (producer.LendOfStream.isImplemented, producer.LproduceElementDone.isImplemented) match {
diff --git a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala
index aa975c8455b..4595e302eb2 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/interfaces/SVoid.scala
@@ -2,12 +2,12 @@ package is.hail.types.physical.stypes.interfaces
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Settable, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.TypeWithRequiredness
 import is.hail.types.physical.PType
 import is.hail.types.physical.stypes._
 import is.hail.types.virtual.{TVoid, Type}
-import is.hail.utils.FastSeq
 
 case object SVoid extends SType {
 
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala
index 0ad1d0d46e8..e526b069a36 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SBoolean.scala
@@ -2,11 +2,11 @@ package is.hail.types.physical.stypes.primitives
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{BooleanInfo, Settable, SettableBuilder, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PBoolean, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.virtual.{TBoolean, Type}
-import is.hail.utils.FastSeq
 
 case object SBoolean extends SPrimitive {
   override def ti: TypeInfo[_] = BooleanInfo
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala
index d53237a2512..cb24f05af7e 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat32.scala
@@ -2,11 +2,11 @@ package is.hail.types.physical.stypes.primitives
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{Code, FloatInfo, Settable, SettableBuilder, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PFloat32, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.virtual.{TFloat32, Type}
-import is.hail.utils.FastSeq
 
 case object SFloat32 extends SPrimitive {
   override def ti: TypeInfo[_] = FloatInfo
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala
index 41e4c9cb555..28f835cebe2 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SFloat64.scala
@@ -3,11 +3,11 @@ package is.hail.types.physical.stypes.primitives
 import is.hail.annotations.Region
 import is.hail.asm4s.{DoubleInfo, Settable, SettableBuilder, TypeInfo, Value}
 import is.hail.asm4s.Code.invokeStatic1
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PFloat64, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.virtual.{TFloat64, Type}
-import is.hail.utils.FastSeq
 
 case object SFloat64 extends SPrimitive {
   override def ti: TypeInfo[_] = DoubleInfo
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala
index f2dcea4340c..e63ce792b40 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt32.scala
@@ -2,11 +2,11 @@ package is.hail.types.physical.stypes.primitives
 
 import is.hail.annotations.Region
 import is.hail.asm4s.{IntInfo, Settable, SettableBuilder, TypeInfo, Value}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PInt32, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.virtual.{TInt32, Type}
-import is.hail.utils.FastSeq
 
 case object SInt32 extends SPrimitive {
   override def ti: TypeInfo[_] = IntInfo
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala
index 27a32ea8fc6..22c5f713f62 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SInt64.scala
@@ -3,11 +3,11 @@ package is.hail.types.physical.stypes.primitives
 import is.hail.annotations.Region
 import is.hail.asm4s.{LongInfo, Settable, SettableBuilder, TypeInfo, Value}
 import is.hail.asm4s.Code.invokeStatic1
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitCodeBuilder
 import is.hail.types.physical.{PInt64, PType}
 import is.hail.types.physical.stypes.{SSettable, SType, SValue}
 import is.hail.types.virtual.{TInt64, Type}
-import is.hail.utils.FastSeq
 
 case object SInt64 extends SPrimitive {
   override def ti: TypeInfo[_] = LongInfo
diff --git a/hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala b/hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala
index aa05e7763d2..3ab9a75d964 100644
--- a/hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala
+++ b/hail/hail/src/is/hail/types/physical/stypes/primitives/SPrimitive.scala
@@ -11,7 +11,7 @@ trait SPrimitive extends SType {
 
   override def copiedType: SType = this
 
-  def containsPointers: Boolean = false
+  override def containsPointers: Boolean = false
 }
 
 abstract class SPrimitiveValue extends SValue {
diff --git a/hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala b/hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala
index 8de6defc0cf..80144f21d42 100644
--- a/hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala
+++ b/hail/hail/src/is/hail/types/virtual/BlockMatrixType.scala
@@ -1,10 +1,9 @@
 package is.hail.types.virtual
 
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs.{I64, If}
 import is.hail.linalg.{BlockMatrix, MatrixSparsity}
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 import is.hail.utils.fatal
 
 import scala.collection.compat._
diff --git a/hail/hail/src/is/hail/types/virtual/MatrixType.scala b/hail/hail/src/is/hail/types/virtual/MatrixType.scala
index c2669d58ca9..26b913f2ac1 100644
--- a/hail/hail/src/is/hail/types/virtual/MatrixType.scala
+++ b/hail/hail/src/is/hail/types/virtual/MatrixType.scala
@@ -1,6 +1,8 @@
 package is.hail.types.virtual
 
 import is.hail.annotations.Annotation
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{Env, IRParser, LowerMatrixIR, MatrixIR, Name}
 import is.hail.types.physical.{PArray, PStruct}
 import is.hail.utils._
@@ -154,7 +156,7 @@ case class MatrixType(
     "g" -> entryType,
   )
 
-  def pretty(sb: StringBuilder, indent0: Int = 0, compact: Boolean = false): Unit = {
+  override def pretty(sb: StringBuilder, indent0: Int = 0, compact: Boolean = false): Unit = {
 
     val space: String = if (compact) "" else " "
     val newline: String = if (compact) "" else "\n"
diff --git a/hail/hail/src/is/hail/types/virtual/TArray.scala b/hail/hail/src/is/hail/types/virtual/TArray.scala
index c037eaa8c10..332804275cb 100644
--- a/hail/hail/src/is/hail/types/virtual/TArray.scala
+++ b/hail/hail/src/is/hail/types/virtual/TArray.scala
@@ -12,7 +12,7 @@ final case class TArray(elementType: Type) extends TContainer {
     sb += '>'
   }
 
-  def _toPretty = s"Array[$elementType]"
+  override def _toPretty = s"Array[$elementType]"
 
   override def canCompare(other: Type): Boolean = other match {
     case TArray(otherType) => elementType.canCompare(otherType)
@@ -32,7 +32,7 @@ final case class TArray(elementType: Type) extends TContainer {
     sb += ']'
   }
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[IndexedSeq[_]] &&
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[IndexedSeq[_]] &&
     a.asInstanceOf[IndexedSeq[_]].forall(elementType.typeCheck)
 
   override def _showStr(a: Annotation): String =
@@ -42,7 +42,7 @@ final case class TArray(elementType: Type) extends TContainer {
 
   override def str(a: Annotation): String = JsonMethods.compact(export(a))
 
-  def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
+  override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.iterableOrdering(elementType.ordering(sm), missingEqual)
 
   override def valueSubsetter(subtype: Type): Any => Any = {
diff --git a/hail/hail/src/is/hail/types/virtual/TBaseStruct.scala b/hail/hail/src/is/hail/types/virtual/TBaseStruct.scala
index 3fd9f17f90b..a243a8f4bd8 100644
--- a/hail/hail/src/is/hail/types/virtual/TBaseStruct.scala
+++ b/hail/hail/src/is/hail/types/virtual/TBaseStruct.scala
@@ -37,7 +37,7 @@ abstract class TBaseStruct extends Type {
 
   def size: Int
 
-  def _toPretty: String = {
+  override def _toPretty: String = {
     val sb = new StringBuilder
     _pretty(sb, 0, compact = true)
     sb.result()
diff --git a/hail/hail/src/is/hail/types/virtual/TBinary.scala b/hail/hail/src/is/hail/types/virtual/TBinary.scala
index d904f538c41..a6c4cbfcb09 100644
--- a/hail/hail/src/is/hail/types/virtual/TBinary.scala
+++ b/hail/hail/src/is/hail/types/virtual/TBinary.scala
@@ -4,11 +4,11 @@ import is.hail.annotations._
 import is.hail.backend.HailStateManager
 
 case object TBinary extends Type {
-  def _toPretty = "Binary"
+  override def _toPretty = "Binary"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Array[Byte]]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Array[Byte]]
 
-  def mkOrdering(sm: HailStateManager, _missingEqual: Boolean = true): ExtendedOrdering =
+  override def mkOrdering(sm: HailStateManager, _missingEqual: Boolean = true): ExtendedOrdering =
     ExtendedOrdering.iterableOrdering(new ExtendedOrdering {
       val missingEqual = _missingEqual
 
diff --git a/hail/hail/src/is/hail/types/virtual/TBoolean.scala b/hail/hail/src/is/hail/types/virtual/TBoolean.scala
index 4035d46402f..a4309630fe8 100644
--- a/hail/hail/src/is/hail/types/virtual/TBoolean.scala
+++ b/hail/hail/src/is/hail/types/virtual/TBoolean.scala
@@ -4,12 +4,12 @@ import is.hail.annotations._
 import is.hail.backend.HailStateManager
 
 case object TBoolean extends Type {
-  def _toPretty = "Boolean"
+  override def _toPretty = "Boolean"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "bool"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Boolean]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Boolean]
 
   override def _showStr(a: Annotation): String = if (a.asInstanceOf[Boolean]) "True" else "False"
 
diff --git a/hail/hail/src/is/hail/types/virtual/TCall.scala b/hail/hail/src/is/hail/types/virtual/TCall.scala
index 39cfe195e93..d68b581ef84 100644
--- a/hail/hail/src/is/hail/types/virtual/TCall.scala
+++ b/hail/hail/src/is/hail/types/virtual/TCall.scala
@@ -5,14 +5,14 @@ import is.hail.backend.HailStateManager
 import is.hail.variant.Call
 
 case object TCall extends Type {
-  def _toPretty = "Call"
+  override def _toPretty = "Call"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "call"
 
   val representation: Type = TInt32
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
 
   override def str(a: Annotation): String =
     if (a == null) "NA" else Call.toString(a.asInstanceOf[Call])
diff --git a/hail/hail/src/is/hail/types/virtual/TDict.scala b/hail/hail/src/is/hail/types/virtual/TDict.scala
index b30851c05fb..37ee672486c 100644
--- a/hail/hail/src/is/hail/types/virtual/TDict.scala
+++ b/hail/hail/src/is/hail/types/virtual/TDict.scala
@@ -2,7 +2,10 @@ package is.hail.types.virtual
 
 import is.hail.annotations.{Annotation, ExtendedOrdering}
 import is.hail.backend.HailStateManager
-import is.hail.utils._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.{toRichMap, toRichOption}
+
+import scala.collection.compat._
 
 import org.json4s.jackson.JsonMethods
 
@@ -25,7 +28,7 @@ final case class TDict(keyType: Type, valueType: Type) extends TContainer {
 
   override def subst() = TDict(keyType.subst(), valueType.subst())
 
-  def _toPretty = s"Dict[$keyType, $valueType]"
+  override def _toPretty = s"Dict[$keyType, $valueType]"
 
   override def pyString(sb: StringBuilder): Unit = {
     sb ++= "dict<"
@@ -43,7 +46,7 @@ final case class TDict(keyType: Type, valueType: Type) extends TContainer {
     sb += ']'
   }
 
-  def _typeCheck(a: Any): Boolean = a == null || (a.isInstanceOf[Map[_, _]] &&
+  override def _typeCheck(a: Any): Boolean = a == null || (a.isInstanceOf[Map[_, _]] &&
     a.asInstanceOf[Map[_, _]].forall { case (k, v) =>
       keyType.typeCheck(k) && valueType.typeCheck(v)
     })
@@ -75,7 +78,7 @@ final case class TDict(keyType: Type, valueType: Type) extends TContainer {
       return identity
 
     val subsetValue = valueType.valueSubsetter(subdict.valueType)
-    (a: Any) => a.asInstanceOf[Map[Any, Any]].mapValues(subsetValue)
+    (a: Any) => a.asInstanceOf[Map[Any, Any]].view.mapValues(subsetValue)
   }
 
   override def arrayElementsRepr: TArray = TArray(elementType)
diff --git a/hail/hail/src/is/hail/types/virtual/TFloat32.scala b/hail/hail/src/is/hail/types/virtual/TFloat32.scala
index 532a1cb7ad0..383d3fa75d1 100644
--- a/hail/hail/src/is/hail/types/virtual/TFloat32.scala
+++ b/hail/hail/src/is/hail/types/virtual/TFloat32.scala
@@ -5,12 +5,12 @@ import is.hail.backend.HailStateManager
 import is.hail.utils._
 
 case object TFloat32 extends TNumeric {
-  def _toPretty = "Float32"
+  override def _toPretty = "Float32"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "float32"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Float]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Float]
 
   override def _showStr(a: Annotation): String = "%.02e".format(a.asInstanceOf[Float])
 
diff --git a/hail/hail/src/is/hail/types/virtual/TFloat64.scala b/hail/hail/src/is/hail/types/virtual/TFloat64.scala
index 9646fd853b0..5fdc15d3b96 100644
--- a/hail/hail/src/is/hail/types/virtual/TFloat64.scala
+++ b/hail/hail/src/is/hail/types/virtual/TFloat64.scala
@@ -10,7 +10,7 @@ case object TFloat64 extends TNumeric {
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "float64"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Double]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Double]
 
   override def _showStr(a: Annotation): String = "%.02e".format(a.asInstanceOf[Double])
 
diff --git a/hail/hail/src/is/hail/types/virtual/TInt32.scala b/hail/hail/src/is/hail/types/virtual/TInt32.scala
index 26bea25deaf..1c1b6095a88 100644
--- a/hail/hail/src/is/hail/types/virtual/TInt32.scala
+++ b/hail/hail/src/is/hail/types/virtual/TInt32.scala
@@ -4,12 +4,12 @@ import is.hail.annotations._
 import is.hail.backend.HailStateManager
 
 case object TInt32 extends TIntegral {
-  def _toPretty = "Int32"
+  override def _toPretty = "Int32"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "int32"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Int]
 
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[Int]], missingEqual)
diff --git a/hail/hail/src/is/hail/types/virtual/TInt64.scala b/hail/hail/src/is/hail/types/virtual/TInt64.scala
index 93f88f000b8..41079d78258 100644
--- a/hail/hail/src/is/hail/types/virtual/TInt64.scala
+++ b/hail/hail/src/is/hail/types/virtual/TInt64.scala
@@ -4,12 +4,12 @@ import is.hail.annotations._
 import is.hail.backend.HailStateManager
 
 case object TInt64 extends TIntegral {
-  def _toPretty = "Int64"
+  override def _toPretty = "Int64"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "int64"
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Long]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Long]
 
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[Long]], missingEqual)
diff --git a/hail/hail/src/is/hail/types/virtual/TInterval.scala b/hail/hail/src/is/hail/types/virtual/TInterval.scala
index be1031e3b46..ee6d5f2684f 100644
--- a/hail/hail/src/is/hail/types/virtual/TInterval.scala
+++ b/hail/hail/src/is/hail/types/virtual/TInterval.scala
@@ -2,13 +2,14 @@ package is.hail.types.virtual
 
 import is.hail.annotations.ExtendedOrdering
 import is.hail.backend.HailStateManager
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.collection.FastSeq
+import is.hail.utils.Interval
 
 case class TInterval(pointType: Type) extends Type {
 
   override def children = FastSeq(pointType)
 
-  def _toPretty = s"""Interval[$pointType]"""
+  override def _toPretty = s"""Interval[$pointType]"""
 
   override def pyString(sb: StringBuilder): Unit = {
     sb ++= "interval<"
@@ -22,7 +23,7 @@ case class TInterval(pointType: Type) extends Type {
     sb += ']'
   }
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Interval] && {
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Interval] && {
     val i = a.asInstanceOf[Interval]
     pointType.typeCheck(i.start) && pointType.typeCheck(i.end)
   }
diff --git a/hail/hail/src/is/hail/types/virtual/TIterable.scala b/hail/hail/src/is/hail/types/virtual/TIterable.scala
index e82a3d72d36..a533f1a68b5 100644
--- a/hail/hail/src/is/hail/types/virtual/TIterable.scala
+++ b/hail/hail/src/is/hail/types/virtual/TIterable.scala
@@ -1,7 +1,7 @@
 package is.hail.types.virtual
 
+import is.hail.collection.FastSeq
 import is.hail.types.BaseType
-import is.hail.utils.FastSeq
 
 abstract class TIterable extends Type {
   def elementType: Type
diff --git a/hail/hail/src/is/hail/types/virtual/TLocus.scala b/hail/hail/src/is/hail/types/virtual/TLocus.scala
index cee504eac00..0002981cccc 100644
--- a/hail/hail/src/is/hail/types/virtual/TLocus.scala
+++ b/hail/hail/src/is/hail/types/virtual/TLocus.scala
@@ -21,14 +21,14 @@ object TLocus {
 
 case class TLocus(rgName: String) extends Type {
 
-  def _toPretty = s"Locus($rgName)"
+  override def _toPretty = s"Locus($rgName)"
 
   def rg: String = rgName
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "locus<" ++= prettyIdentifier(rgName) += '>': Unit
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[Locus]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[Locus]
 
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean = true): ExtendedOrdering =
     sm.referenceGenomes(rgName).extendedLocusOrdering
diff --git a/hail/hail/src/is/hail/types/virtual/TNDArray.scala b/hail/hail/src/is/hail/types/virtual/TNDArray.scala
index eb769c310a1..1221fc12d4d 100644
--- a/hail/hail/src/is/hail/types/virtual/TNDArray.scala
+++ b/hail/hail/src/is/hail/types/virtual/TNDArray.scala
@@ -46,7 +46,7 @@ final case class TNDArray(elementType: Type, nDimsBase: NatBase) extends Type {
     sb += '>'
   }
 
-  def _toPretty = s"NDArray[$elementType,$nDims]"
+  override def _toPretty = s"NDArray[$elementType,$nDims]"
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
     sb ++= "NDArray["
@@ -105,7 +105,7 @@ final case class TNDArray(elementType: Type, nDimsBase: NatBase) extends Type {
 
   override def subst(): TNDArray = TNDArray(elementType.subst(), nDimsBase.subst())
 
-  def _typeCheck(a: Annotation): Boolean = a match {
+  override def _typeCheck(a: Annotation): Boolean = a match {
     case nd: NDArray => nd.forall(e => elementType.typeCheck(e))
     case _ => false
   }
diff --git a/hail/hail/src/is/hail/types/virtual/TRNGState.scala b/hail/hail/src/is/hail/types/virtual/TRNGState.scala
index b9b25283658..3ce9fada0a8 100644
--- a/hail/hail/src/is/hail/types/virtual/TRNGState.scala
+++ b/hail/hail/src/is/hail/types/virtual/TRNGState.scala
@@ -8,9 +8,9 @@ case object TRNGState extends Type {
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "rng_state"
 
-  def _typeCheck(a: Any): Boolean = ???
+  override def _typeCheck(a: Any): Boolean = ???
 
-  def mkOrdering(sm: HailStateManager, missingEqual: Boolean)
+  override def mkOrdering(sm: HailStateManager, missingEqual: Boolean)
     : is.hail.annotations.ExtendedOrdering = ???
 
   override def isIsomorphicTo(t: Type): Boolean =
diff --git a/hail/hail/src/is/hail/types/virtual/TSet.scala b/hail/hail/src/is/hail/types/virtual/TSet.scala
index 98a2282fbc0..f0ed6561167 100644
--- a/hail/hail/src/is/hail/types/virtual/TSet.scala
+++ b/hail/hail/src/is/hail/types/virtual/TSet.scala
@@ -6,7 +6,7 @@ import is.hail.backend.HailStateManager
 import org.json4s.jackson.JsonMethods
 
 final case class TSet(elementType: Type) extends TContainer {
-  def _toPretty = s"Set[$elementType]"
+  override def _toPretty = s"Set[$elementType]"
 
   override def pyString(sb: StringBuilder): Unit = {
     sb ++= "set<"
@@ -26,7 +26,7 @@ final case class TSet(elementType: Type) extends TContainer {
 
   override def subst() = TSet(elementType.subst())
 
-  def _typeCheck(a: Any): Boolean =
+  override def _typeCheck(a: Any): Boolean =
     a.isInstanceOf[Set[_]] && a.asInstanceOf[Set[_]].forall(elementType.typeCheck)
 
   override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean = false): Unit = {
diff --git a/hail/hail/src/is/hail/types/virtual/TStream.scala b/hail/hail/src/is/hail/types/virtual/TStream.scala
index b5186a350a1..679215610cd 100644
--- a/hail/hail/src/is/hail/types/virtual/TStream.scala
+++ b/hail/hail/src/is/hail/types/virtual/TStream.scala
@@ -12,7 +12,7 @@ final case class TStream(elementType: Type) extends TIterable {
     sb += '>'
   }
 
-  def _toPretty = s"Stream[$elementType]"
+  override def _toPretty = s"Stream[$elementType]"
 
   override def canCompare(other: Type): Boolean =
     throw new UnsupportedOperationException("Stream comparison is currently undefined.")
@@ -30,7 +30,7 @@ final case class TStream(elementType: Type) extends TIterable {
     sb += ']'
   }
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[IndexedSeq[_]] &&
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[IndexedSeq[_]] &&
     a.asInstanceOf[IndexedSeq[_]].forall(elementType.typeCheck)
 
   override def str(a: Annotation): String = JsonMethods.compact(export(a))
diff --git a/hail/hail/src/is/hail/types/virtual/TString.scala b/hail/hail/src/is/hail/types/virtual/TString.scala
index 6f7e99211d0..1204beeb444 100644
--- a/hail/hail/src/is/hail/types/virtual/TString.scala
+++ b/hail/hail/src/is/hail/types/virtual/TString.scala
@@ -4,14 +4,14 @@ import is.hail.annotations._
 import is.hail.backend.HailStateManager
 
 case object TString extends Type {
-  def _toPretty = "String"
+  override def _toPretty = "String"
 
   override def pyString(sb: StringBuilder): Unit =
     sb ++= "str"
 
   override def _showStr(a: Annotation): String = "\"" + a.asInstanceOf[String] + "\""
 
-  def _typeCheck(a: Any): Boolean = a.isInstanceOf[String]
+  override def _typeCheck(a: Any): Boolean = a.isInstanceOf[String]
 
   override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering =
     ExtendedOrdering.extendToNull(implicitly[Ordering[String]], missingEqual)
diff --git a/hail/hail/src/is/hail/types/virtual/TStruct.scala b/hail/hail/src/is/hail/types/virtual/TStruct.scala
index f28bad29363..6ccdc1da93c 100644
--- a/hail/hail/src/is/hail/types/virtual/TStruct.scala
+++ b/hail/hail/src/is/hail/types/virtual/TStruct.scala
@@ -2,10 +2,11 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{Env, IRParser, Name}
+import is.hail.sparkextras.implicits.toRichRow
 import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -65,7 +66,7 @@ final case class TStruct(fields: IndexedSeq[Field]) extends TBaseStruct {
     }
   }
 
-  def size: Int = fields.length
+  override def size: Int = fields.length
 
   override def truncate(newSize: Int): TStruct = TStruct(fields.take(newSize))
 
@@ -296,7 +297,7 @@ final case class TStruct(fields: IndexedSeq[Field]) extends TBaseStruct {
       ab += fields(i)
       i += 1
     }
-    val it = fieldsToInsert.toIterator
+    val it = fieldsToInsert.iterator
     while (it.hasNext) {
       val (name, typ) = it.next()
       if (fieldIdx.contains(name)) {
diff --git a/hail/hail/src/is/hail/types/virtual/TTuple.scala b/hail/hail/src/is/hail/types/virtual/TTuple.scala
index 8c4917430d7..79f152b25bb 100644
--- a/hail/hail/src/is/hail/types/virtual/TTuple.scala
+++ b/hail/hail/src/is/hail/types/virtual/TTuple.scala
@@ -2,7 +2,7 @@ package is.hail.types.virtual
 
 import is.hail.annotations.ExtendedOrdering
 import is.hail.backend.HailStateManager
-import is.hail.utils._
+import is.hail.collection.implicits.toRichIterable
 
 import scala.collection.compat._
 
@@ -34,7 +34,7 @@ final case class TTuple(_types: IndexedSeq[TupleField]) extends TBaseStruct {
 
   override lazy val _isCanonical: Boolean = _types.indices.forall(i => i == _types(i).index)
 
-  def size: Int = types.length
+  override def size: Int = types.length
 
   override def truncate(newSize: Int): TTuple =
     TTuple(_types.take(newSize))
diff --git a/hail/hail/src/is/hail/types/virtual/TUnion.scala b/hail/hail/src/is/hail/types/virtual/TUnion.scala
deleted file mode 100644
index 88e7a7335d1..00000000000
--- a/hail/hail/src/is/hail/types/virtual/TUnion.scala
+++ /dev/null
@@ -1,134 +0,0 @@
-package is.hail.types.virtual
-
-import is.hail.annotations.ExtendedOrdering
-import is.hail.backend.HailStateManager
-import is.hail.expr.ir.IRParser
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
-
-import scala.collection.compat._
-
-import org.json4s.CustomSerializer
-import org.json4s.JsonAST.JString
-
-final case class Case(name: String, typ: Type, index: Int) {
-
-  def unify(cf: Case): Boolean =
-    name == cf.name &&
-      typ.unify(cf.typ) &&
-      index == cf.index
-
-  def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
-    if (compact) {
-      sb.append(prettyIdentifier(name))
-      sb.append(":")
-    } else {
-      sb.append(" " * indent)
-      sb.append(prettyIdentifier(name))
-      sb.append(": ")
-    }
-    typ.pretty(sb, indent, compact)
-  }
-}
-
-class TUnionSerializer extends CustomSerializer[TUnion](format =>
-      (
-        { case JString(s) => IRParser.parseUnionType(s) },
-        { case t: TUnion => JString(t.parsableString()) },
-      )
-    )
-
-object TUnion {
-  val empty: TUnion = TUnion(FastSeq())
-
-  def apply(args: (String, Type)*): TUnion =
-    TUnion(args
-      .iterator
-      .zipWithIndex
-      .map { case ((n, t), i) => Case(n, t, i) }
-      .toArray)
-}
-
-final case class TUnion(cases: IndexedSeq[Case]) extends Type {
-  lazy val types: Array[Type] = cases.map(_.typ).toArray
-
-  lazy val caseIdx: collection.Map[String, Int] = toMapFast(cases)(_.name, _.index)
-
-  lazy val caseNames: Array[String] = cases.map(_.name).toArray
-
-  def size: Int = cases.length
-
-  override def unify(concrete: Type): Boolean = concrete match {
-    case TUnion(cfields) =>
-      cases.length == cfields.length &&
-      cases.lazyZip(cfields).forall { case (f, cf) =>
-        f.unify(cf)
-      }
-    case _ => false
-  }
-
-  override def subst(): TUnion = TUnion(cases.map(f => f.copy(typ = f.typ.subst())))
-
-  def index(str: String): Option[Int] = caseIdx.get(str)
-
-  def selfCase(name: String): Option[Case] = caseIdx.get(name).map(i => cases(i))
-
-  def hasCase(name: String): Boolean = caseIdx.contains(name)
-
-  def getCase(name: String): Case = cases(caseIdx(name))
-
-  def fieldType(name: String): Type = types(caseIdx(name))
-
-  def rename(m: Map[String, String]): TUnion = {
-    val newFieldsBuilder = ArraySeq.newBuilder[(String, Type)]
-    cases.foreach { fd =>
-      val n = fd.name
-      newFieldsBuilder += (m.getOrElse(n, n) -> fd.typ)
-    }
-    TUnion(newFieldsBuilder.result(): _*)
-  }
-
-  def _toPretty: String = {
-    val sb = new StringBuilder
-    _pretty(sb, 0, compact = true)
-    sb.result()
-  }
-
-  override def _typeCheck(a: Any): Boolean = ???
-
-  override def pyString(sb: StringBuilder): Unit = {
-    sb ++= "union{"
-    cases.foreachBetween({ field =>
-      sb ++= prettyIdentifier(field.name) ++= ": ": Unit
-      field.typ.pyString(sb)
-    })(sb ++= ", ")
-    sb += '}'
-  }
-
-  override def _pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit = {
-    if (compact) {
-      sb ++= "Union{"
-      cases.foreachBetween(_.pretty(sb, indent, compact))(sb += ',')
-      sb += '}'
-    } else {
-      if (size == 0)
-        sb ++= "Union { }"
-      else {
-        sb ++= "Union {\n"
-        cases.foreachBetween(_.pretty(sb, indent + 4, compact))(sb ++= ",\n")
-        sb += '\n' ++= (" " * indent) += '}': Unit
-      }
-    }
-  }
-
-  override def mkOrdering(sm: HailStateManager, missingEqual: Boolean): ExtendedOrdering = ???
-
-  override def isIsomorphicTo(t: Type): Boolean =
-    t match {
-      case u: TUnion =>
-        size == u.size &&
-        cases.lazyZip(u.cases).forall(_.typ isIsomorphicTo _.typ)
-      case _ =>
-        false
-    }
-}
diff --git a/hail/hail/src/is/hail/types/virtual/TVariable.scala b/hail/hail/src/is/hail/types/virtual/TVariable.scala
index fa647f19c8e..f65a2092675 100644
--- a/hail/hail/src/is/hail/types/virtual/TVariable.scala
+++ b/hail/hail/src/is/hail/types/virtual/TVariable.scala
@@ -53,7 +53,7 @@ final case class TVariable(name: String, cond: String = null) extends Type {
 
   override def isRealizable = false
 
-  def _typeCheck(a: Any): Boolean =
+  override def _typeCheck(a: Any): Boolean =
     throw new RuntimeException("TVariable is not realizable")
 
   override def unify(concrete: Type): Boolean =
diff --git a/hail/hail/src/is/hail/types/virtual/TableType.scala b/hail/hail/src/is/hail/types/virtual/TableType.scala
index 4129f8c7978..f06b0ba7c9c 100644
--- a/hail/hail/src/is/hail/types/virtual/TableType.scala
+++ b/hail/hail/src/is/hail/types/virtual/TableType.scala
@@ -1,5 +1,7 @@
 package is.hail.types.virtual
 
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir._
 import is.hail.rvd.RVDType
 import is.hail.types.physical.{PStruct, PType}
@@ -55,7 +57,7 @@ case class TableType(rowType: TStruct, key: IndexedSeq[String], globalType: TStr
   lazy val valueType: TStruct = TableType.valueType(rowType, key)
   def valueFieldIdx: Array[Int] = canonicalRVDType.valueFieldIdx
 
-  def pretty(sb: StringBuilder, indent0: Int = 0, compact: Boolean = false): Unit = {
+  override def pretty(sb: StringBuilder, indent0: Int = 0, compact: Boolean = false): Unit = {
 
     val space: String = if (compact) "" else " "
     val padding: String = if (compact) "" else " " * indent0
diff --git a/hail/hail/src/is/hail/types/virtual/Type.scala b/hail/hail/src/is/hail/types/virtual/Type.scala
index d5423df108a..ef8edab3efa 100644
--- a/hail/hail/src/is/hail/types/virtual/Type.scala
+++ b/hail/hail/src/is/hail/types/virtual/Type.scala
@@ -2,10 +2,10 @@ package is.hail.types.virtual
 
 import is.hail.annotations._
 import is.hail.backend.HailStateManager
+import is.hail.collection.FastSeq
 import is.hail.expr.{JSONAnnotationImpex, SparkAnnotationImpex}
 import is.hail.expr.ir._
 import is.hail.utils
-import is.hail.utils._
 
 import org.apache.spark.sql.types.DataType
 import org.json4s.{CustomSerializer, JValue}
@@ -53,7 +53,7 @@ abstract class Type extends VType with Serializable {
     else
       (this, identity[Annotation])
 
-  final def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
+  final override def pretty(sb: StringBuilder, indent: Int, compact: Boolean): Unit =
     _pretty(sb, indent, compact)
 
   def _toPretty: String
diff --git a/hail/hail/src/is/hail/utils/AbsoluteFuzzyComparable.scala b/hail/hail/src/is/hail/utils/AbsoluteFuzzyComparable.scala
deleted file mode 100644
index 3709b4f9b0e..00000000000
--- a/hail/hail/src/is/hail/utils/AbsoluteFuzzyComparable.scala
+++ /dev/null
@@ -1,23 +0,0 @@
-package is.hail.utils
-
-trait AbsoluteFuzzyComparable[A] {
-  def absoluteEq(tolerance: Double, x: A, y: A): Boolean
-}
-
-object AbsoluteFuzzyComparable {
-
-  def absoluteEq[T](tolerance: Double, x: T, y: T)(implicit afc: AbsoluteFuzzyComparable[T])
-    : Boolean =
-    afc.absoluteEq(tolerance, x, y)
-
-  implicit object afcDoubles extends AbsoluteFuzzyComparable[Double] {
-    def absoluteEq(tolerance: Double, x: Double, y: Double) = Math.abs(x - y) <= tolerance
-  }
-
-  implicit def afcMaps[K, V](implicit vRFC: AbsoluteFuzzyComparable[V])
-    : AbsoluteFuzzyComparable[Map[K, V]] =
-    new AbsoluteFuzzyComparable[Map[K, V]] {
-      def absoluteEq(tolerance: Double, x: Map[K, V], y: Map[K, V]) =
-        x.keySet == y.keySet && x.keys.forall(k => vRFC.absoluteEq(tolerance, x(k), y(k)))
-    }
-}
diff --git a/hail/hail/src/is/hail/utils/Bitstring.scala b/hail/hail/src/is/hail/utils/Bitstring.scala
deleted file mode 100644
index 05f2984f198..00000000000
--- a/hail/hail/src/is/hail/utils/Bitstring.scala
+++ /dev/null
@@ -1,90 +0,0 @@
-package is.hail.utils
-
-import is.hail.utils.compat.immutable.ArraySeq
-
-import scala.collection.mutable
-
-object Bitstring {
-  def apply(string: String): Bitstring = {
-    assert(string.forall(c => c == '0' || c == '1'))
-    val bitstring = ArraySeq.newBuilder[Long]
-    var pos: Int = 0
-    while (string.length - pos > 64) {
-      bitstring += java.lang.Long.parseUnsignedLong(string.slice(pos, pos + 64), 2)
-      pos += 64
-    }
-    val lastWord = java.lang.Long.parseUnsignedLong(string.slice(pos, string.length))
-    val bitsInLastWord = string.length - pos
-    bitstring += (lastWord << (64 - bitsInLastWord))
-    new Bitstring(bitstring.result(), bitsInLastWord)
-  }
-}
-
-case class Bitstring(contents: IndexedSeq[Long], bitsInLastWord: Int) {
-  def numWords = contents.length
-  def length = (contents.length - 1) * 64 + bitsInLastWord
-
-  override def toString: String = {
-    if (contents.isEmpty) return "Bitstring()"
-    val result = new mutable.StringBuilder("Bitstring(")
-    var i = 0
-    while (i < contents.length - 1) {
-      result ++= contents(i).toBinaryString
-      i += 1
-    }
-    i = 0
-    var lastWord = contents.last
-    val bits = Array('0', '1')
-    while (i < bitsInLastWord) {
-      result += bits((lastWord >>> 63).toInt)
-      lastWord <<= 1
-      i += 1
-    }
-    result += ')'
-    result.result()
-  }
-
-  def ++(rhs: Bitstring): Bitstring = {
-    if (length == 0) return rhs
-    if (rhs.length == 0) return this
-    if (bitsInLastWord < 64) {
-      val newNumWords = (length + rhs.length + 63) >> 6
-      val newContents = Array.ofDim[Long](newNumWords)
-      for (i <- 0 until (numWords - 2))
-        newContents(i) = contents(i)
-      newContents(numWords - 1) = contents.last & (rhs.contents.head >>> bitsInLastWord)
-      for (i <- 0 until (rhs.numWords - 2))
-        newContents(numWords + i) =
-          (rhs.contents(i) << (64 - bitsInLastWord)) &
-            (rhs.contents(i + 1) >>> bitsInLastWord)
-      var newBitsInLastWord = bitsInLastWord + rhs.bitsInLastWord
-      if (newBitsInLastWord > 64) {
-        newContents(numWords + rhs.numWords - 1) = rhs.contents.last << (64 - bitsInLastWord)
-        newBitsInLastWord = newBitsInLastWord - 64
-      }
-      new Bitstring(newContents, newBitsInLastWord)
-    } else {
-      new Bitstring(contents ++ rhs.contents, rhs.bitsInLastWord)
-    }
-  }
-
-  def popWords(n: Int): (Array[Long], Bitstring) = {
-    assert(n < numWords || (n == numWords && bitsInLastWord == 64))
-    val result = contents.slice(0, n).toArray
-    val newContents = contents.slice(n, numWords)
-    val newBitsInLastWord = if (n < numWords) bitsInLastWord else 0
-    (result, new Bitstring(newContents, newBitsInLastWord))
-  }
-
-  def padTo(n: Int): Array[Long] = {
-    assert(n > numWords || (n == numWords && bitsInLastWord < 64))
-    val result = Array.ofDim[Long](n)
-    Array.copy(contents, 0, result, 0, numWords)
-    if (bitsInLastWord == 64) {
-      result(numWords) = 1L << 63
-    } else {
-      result(numWords - 1) = result(numWords - 1) & (1L << (63 - bitsInLastWord))
-    }
-    result
-  }
-}
diff --git a/hail/hail/src/is/hail/utils/Cache.scala b/hail/hail/src/is/hail/utils/Cache.scala
index f0216a50323..5712aac46d0 100644
--- a/hail/hail/src/is/hail/utils/Cache.scala
+++ b/hail/hail/src/is/hail/utils/Cache.scala
@@ -1,7 +1,7 @@
 package is.hail.utils
 
 import is.hail.annotations.{Region, RegionMemory}
-import is.hail.utils.compat.mutable.{GrowableCompat, ShrinkableCompat}
+import is.hail.collection.compat.mutable.{GrowableCompat, ShrinkableCompat}
 
 import scala.collection.mutable
 import scala.jdk.CollectionConverters._
@@ -66,5 +66,5 @@ class LongToRegionValueCache(capacity: Int) extends Closeable {
     m.clear()
   }
 
-  def close(): Unit = free()
+  override def close(): Unit = free()
 }
diff --git a/hail/hail/src/is/hail/utils/EitherIsAMonad.scala b/hail/hail/src/is/hail/utils/EitherIsAMonad.scala
deleted file mode 100644
index cd0809966a1..00000000000
--- a/hail/hail/src/is/hail/utils/EitherIsAMonad.scala
+++ /dev/null
@@ -1,38 +0,0 @@
-package is.hail.utils
-
-object EitherIsAMonad {
-  implicit def eitherIsAMonad[A, B](eab: Either[A, B]): EitherOps[A, B] = new EitherOps(eab)
-}
-
-final class EitherOps[A, B](val eab: Either[A, B]) extends AnyVal {
-  def foreach(f: B => Unit): Unit = eab match {
-    case Left(_) => ()
-    case Right(b) => f(b)
-  }
-
-  def getOrElse(default: => B): B = eab match {
-    case Left(_) => default
-    case Right(b) => b
-  }
-
-  def valueOr(f: A => B): B = eab match {
-    case Left(a) => f(a)
-    case Right(b) => b
-  }
-
-  def toOption: Option[B] = eab match {
-    case Left(_) => None
-    case Right(b) => Some(b)
-  }
-
-  def map[C](f: B => C): Either[A, C] = eab match {
-    case l @ Left(_) => l.asInstanceOf[Either[A, C]]
-    case Right(b) => Right(f(b))
-  }
-
-  def flatMap[D](f: B => Either[A, D]): Either[A, D] = eab match {
-    case l @ Left(_) => l.asInstanceOf[Either[A, D]]
-    case Right(b) => f(b)
-  }
-
-}
diff --git a/hail/hail/src/is/hail/utils/Graph.scala b/hail/hail/src/is/hail/utils/Graph.scala
index 478acac0b75..1efecca497c 100644
--- a/hail/hail/src/is/hail/utils/Graph.scala
+++ b/hail/hail/src/is/hail/utils/Graph.scala
@@ -3,6 +3,7 @@ package is.hail.utils
 import is.hail.annotations.{Region, RegionValueBuilder, UnsafeIndexedSeq}
 import is.hail.asm4s._
 import is.hail.backend.{HailStateManager, HailTaskContext}
+import is.hail.collection.BinaryHeap
 import is.hail.io.fs.FS
 import is.hail.types.physical.PTuple
 import is.hail.variant.ReferenceGenome
diff --git a/hail/hail/src/is/hail/utils/HTTPClient.scala b/hail/hail/src/is/hail/utils/HTTPClient.scala
deleted file mode 100644
index 044f93360e3..00000000000
--- a/hail/hail/src/is/hail/utils/HTTPClient.scala
+++ /dev/null
@@ -1,68 +0,0 @@
-package is.hail.utils
-
-import java.io.{InputStream, OutputStream}
-import java.net.{HttpURLConnection, URL}
-import java.nio.charset.StandardCharsets
-
-import org.apache.commons.io.output.ByteArrayOutputStream
-
-object HTTPClient {
-  def post[T](
-    url: String,
-    contentLength: Int,
-    writeBody: OutputStream => Unit,
-    readResponse: InputStream => T = (_: InputStream) => (),
-    chunkSize: Int = 0,
-  ): T = {
-    val conn = new URL(url).openConnection().asInstanceOf[HttpURLConnection]
-    conn.setRequestMethod("POST")
-    if (chunkSize > 0)
-      conn.setChunkedStreamingMode(chunkSize)
-    conn.setDoOutput(true);
-    conn.setRequestProperty("Content-Length", Integer.toString(contentLength))
-    using(conn.getOutputStream())(writeBody)
-    assert(
-      200 <= conn.getResponseCode() && conn.getResponseCode() < 300,
-      s"POST $url ${conn.getResponseCode()} ${using(conn.getErrorStream())(fullyReadInputStreamAsString)}",
-    )
-    val result = using(conn.getInputStream())(readResponse)
-    conn.disconnect()
-    result
-  }
-
-  def get[T](
-    url: String,
-    readResponse: InputStream => T,
-  ): T = {
-    val conn = new URL(url).openConnection().asInstanceOf[HttpURLConnection]
-    conn.setRequestMethod("GET")
-    assert(
-      200 <= conn.getResponseCode() && conn.getResponseCode() < 300,
-      s"GET $url ${conn.getResponseCode()} ${using(conn.getErrorStream())(fullyReadInputStreamAsString)}",
-    )
-    val result = using(conn.getInputStream())(readResponse)
-    conn.disconnect()
-    result
-  }
-
-  def delete(
-    url: String,
-    readResponse: InputStream => Unit = (_: InputStream) => (),
-  ): Unit = {
-    val conn = new URL(url).openConnection().asInstanceOf[HttpURLConnection]
-    conn.setRequestMethod("DELETE")
-    assert(
-      200 <= conn.getResponseCode() && conn.getResponseCode() < 300,
-      s"DELETE $url ${conn.getResponseCode()} ${using(conn.getErrorStream())(fullyReadInputStreamAsString)}",
-    )
-    val result = using(conn.getInputStream())(readResponse)
-    conn.disconnect()
-    result
-  }
-
-  private[this] def fullyReadInputStreamAsString(is: InputStream): String =
-    using(new ByteArrayOutputStream()) { baos =>
-      drainInputStreamToOutputStream(is, baos)
-      new String(baos.toByteArray(), StandardCharsets.UTF_8)
-    }
-}
diff --git a/hail/hail/src/is/hail/utils/HailIterator.scala b/hail/hail/src/is/hail/utils/HailIterator.scala
deleted file mode 100644
index f1c0b57f26c..00000000000
--- a/hail/hail/src/is/hail/utils/HailIterator.scala
+++ /dev/null
@@ -1,25 +0,0 @@
-package is.hail.utils
-
-import scala.collection.mutable
-import scala.reflect.ClassTag
-
-abstract class HailIterator[@specialized T] {
-  def next(): T
-
-  def hasNext: Boolean
-
-  def toArray(implicit tct: ClassTag[T]): Array[T] = {
-    val b = new mutable.ArrayBuffer[T]()
-    while (hasNext)
-      b += next()
-    b.toArray
-  }
-
-  def countNonNegative()(implicit ev: Numeric[T]): Int = {
-    import ev._
-    var count = 0
-    while (hasNext)
-      if (next() >= ev.zero) count += 1
-    count
-  }
-}
diff --git a/hail/hail/src/is/hail/utils/Interval.scala b/hail/hail/src/is/hail/utils/Interval.scala
index 976e96158b3..ceaee37997f 100644
--- a/hail/hail/src/is/hail/utils/Interval.scala
+++ b/hail/hail/src/is/hail/utils/Interval.scala
@@ -1,8 +1,9 @@
 package is.hail.utils
 
 import is.hail.annotations._
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.sparkextras.implicits.toRichRow
 import is.hail.types.virtual.TBoolean
-import is.hail.utils.compat.immutable.ArraySeq
 
 import org.apache.spark.sql.Row
 import org.json4s.JValue
@@ -275,4 +276,12 @@ object Interval {
     }
     ab.result()
   }
+
+  def ordMax[T](left: T, right: T, ord: ExtendedOrdering): T =
+    if (ord.gt(left, right)) left
+    else right
+
+  def ordMin[T](left: T, right: T, ord: ExtendedOrdering): T =
+    if (ord.lt(left, right)) left
+    else right
 }
diff --git a/hail/hail/src/is/hail/utils/JSON.scala b/hail/hail/src/is/hail/utils/JSON.scala
deleted file mode 100644
index 260fc1acb37..00000000000
--- a/hail/hail/src/is/hail/utils/JSON.scala
+++ /dev/null
@@ -1,13 +0,0 @@
-package is.hail.utils
-
-import org.json4s.JValue
-
-trait JSONWriter[T] {
-  def toJSON(x: T): JValue
-}
-
-trait JSONReader[T] {
-  def fromJSON(jv: JValue): T
-}
-
-trait JSONReaderWriter[T] extends JSONReader[T] with JSONWriter[T]
diff --git a/hail/hail/src/is/hail/utils/NumericImplicits.scala b/hail/hail/src/is/hail/utils/NumericImplicits.scala
deleted file mode 100644
index 047cacab411..00000000000
--- a/hail/hail/src/is/hail/utils/NumericImplicits.scala
+++ /dev/null
@@ -1,52 +0,0 @@
-package is.hail.utils
-
-import breeze.linalg.{DenseVector => BDenseVector, SparseVector => BSparseVector, Vector => BVector}
-import breeze.linalg.operators.{OpAdd, OpSub}
-import org.apache.spark.mllib.linalg.{
-  DenseVector => SDenseVector, SparseVector => SSparseVector, Vector => SVector,
-}
-import org.apache.spark.mllib.linalg.distributed.IndexedRow
-
-trait NumericImplicits {
-
-  implicit def toBDenseVector(v: SDenseVector): BDenseVector[Double] = new BDenseVector(v.values)
-
-  implicit def toBSparseVector(v: SSparseVector): BSparseVector[Double] =
-    new BSparseVector(v.indices, v.values, v.size)
-
-  implicit def toBVector(v: SVector): BVector[Double] = v match {
-    case v: SSparseVector => v
-    case v: SDenseVector => v
-  }
-
-  implicit def toSDenseVector(v: BDenseVector[Double]): SDenseVector = new SDenseVector(v.toArray)
-
-  implicit def toSSparseVector(v: BSparseVector[Double]): SSparseVector =
-    new SSparseVector(v.length, v.array.index, v.array.data)
-
-  implicit def toSVector(v: BVector[Double]): SVector = v match {
-    case v: BDenseVector[Double] => v
-    case v: BSparseVector[Double] => v
-  }
-
-  implicit object subBVectorSVector extends OpSub.Impl2[BVector[Double], SVector, BVector[Double]] {
-    def apply(a: BVector[Double], b: SVector): BVector[Double] = a - toBVector(b)
-  }
-
-  implicit object subBVectorIndexedRow
-      extends OpSub.Impl2[BVector[Double], IndexedRow, IndexedRow] {
-    def apply(a: BVector[Double], b: IndexedRow): IndexedRow =
-      IndexedRow(b.index, a - toBVector(b.vector))
-  }
-
-  implicit object addBVectorSVector extends OpAdd.Impl2[BVector[Double], SVector, BVector[Double]] {
-    def apply(a: BVector[Double], b: SVector): BVector[Double] = a + toBVector(b)
-  }
-
-  implicit object addBVectorIndexedRow
-      extends OpAdd.Impl2[BVector[Double], IndexedRow, IndexedRow] {
-    def apply(a: BVector[Double], b: IndexedRow): IndexedRow =
-      IndexedRow(b.index, a + toBVector(b.vector))
-  }
-
-}
diff --git a/hail/hail/src/is/hail/utils/NumericPair.scala b/hail/hail/src/is/hail/utils/NumericPair.scala
deleted file mode 100644
index ebb0876e9c5..00000000000
--- a/hail/hail/src/is/hail/utils/NumericPair.scala
+++ /dev/null
@@ -1,49 +0,0 @@
-package is.hail.utils
-
-trait NumericPair[T, BoxedT >: Null] extends Serializable {
-
-  def box(t: T): BoxedT
-
-  def unbox(u: BoxedT): T
-
-  implicit val numeric: scala.math.Numeric[T]
-}
-
-trait NumericPairImplicits {
-
-  implicit object IntPair extends NumericPair[Int, java.lang.Integer] {
-
-    def box(t: Int): java.lang.Integer = Int.box(t)
-
-    def unbox(u: java.lang.Integer): Int = Int.unbox(u)
-
-    val numeric: scala.math.Numeric[Int] = implicitly[Numeric[Int]]
-  }
-
-  implicit object LongPair extends NumericPair[Long, java.lang.Long] {
-
-    def box(t: Long): java.lang.Long = Long.box(t)
-
-    def unbox(u: java.lang.Long): Long = Long.unbox(u)
-
-    val numeric: scala.math.Numeric[Long] = implicitly[Numeric[Long]]
-  }
-
-  implicit object FloatPair extends NumericPair[Float, java.lang.Float] {
-
-    def box(t: Float): java.lang.Float = Float.box(t)
-
-    def unbox(u: java.lang.Float): Float = Float.unbox(u)
-
-    val numeric: scala.math.Numeric[Float] = implicitly[Numeric[Float]]
-  }
-
-  implicit object DoublePair extends NumericPair[Double, java.lang.Double] {
-
-    def box(t: Double): java.lang.Double = Double.box(t)
-
-    def unbox(u: java.lang.Double): Double = Double.unbox(u)
-
-    val numeric: scala.math.Numeric[Double] = implicitly[Numeric[Double]]
-  }
-}
diff --git a/hail/hail/src/is/hail/utils/PartitionCounts.scala b/hail/hail/src/is/hail/utils/PartitionCounts.scala
index 1ddc6d990a7..225313cfbba 100644
--- a/hail/hail/src/is/hail/utils/PartitionCounts.scala
+++ b/hail/hail/src/is/hail/utils/PartitionCounts.scala
@@ -35,7 +35,7 @@ object PartitionCounts {
   def getTailPCs(original: IndexedSeq[Long], n: Long): IndexedSeq[Long] =
     getPCSubsetOffset(n, original.reverseIterator) match {
       case Some(PCSubsetOffset(lastIdx, nKeep, _)) =>
-        (0 to lastIdx).reverseMap { i =>
+        (0 to lastIdx).reverse.map { i =>
           if (i == lastIdx)
             nKeep
           else
diff --git a/hail/hail/src/is/hail/utils/RelativeFuzzyComparable.scala b/hail/hail/src/is/hail/utils/RelativeFuzzyComparable.scala
deleted file mode 100644
index 5cc572e6b2c..00000000000
--- a/hail/hail/src/is/hail/utils/RelativeFuzzyComparable.scala
+++ /dev/null
@@ -1,23 +0,0 @@
-package is.hail.utils
-
-trait RelativeFuzzyComparable[A] {
-  def relativeEq(tolerance: Double, x: A, y: A): Boolean
-}
-
-object RelativeFuzzyComparable {
-
-  def relativeEq[T](tolerance: Double, x: T, y: T)(implicit afc: RelativeFuzzyComparable[T])
-    : Boolean =
-    afc.relativeEq(tolerance, x, y)
-
-  implicit object rfcDoubles extends RelativeFuzzyComparable[Double] {
-    def relativeEq(tolerance: Double, x: Double, y: Double) = D_==(x, y, tolerance)
-  }
-
-  implicit def rfcMaps[K, V](implicit vRFC: RelativeFuzzyComparable[V])
-    : RelativeFuzzyComparable[Map[K, V]] =
-    new RelativeFuzzyComparable[Map[K, V]] {
-      def relativeEq(tolerance: Double, x: Map[K, V], y: Map[K, V]) =
-        x.keySet == y.keySet && x.keys.forall(k => vRFC.relativeEq(tolerance, x(k), y(k)))
-    }
-}
diff --git a/hail/hail/src/is/hail/utils/SpillingCollectIterator.scala b/hail/hail/src/is/hail/utils/SpillingCollectIterator.scala
index 07bc110528d..07b48263b1f 100644
--- a/hail/hail/src/is/hail/utils/SpillingCollectIterator.scala
+++ b/hail/hail/src/is/hail/utils/SpillingCollectIterator.scala
@@ -70,7 +70,7 @@ class SpillingCollectIterator[T: ClassTag] private (
     }
   }
 
-  def hasNext: Boolean = {
+  override def hasNext: Boolean = {
     if (it == null || !it.hasNext) {
       if (i >= files.length) {
         it = null
@@ -100,7 +100,7 @@ class SpillingCollectIterator[T: ClassTag] private (
     it.hasNext
   }
 
-  def next(): T = {
+  override def next(): T = {
     hasNext: Unit
     it.next()
   }
diff --git a/hail/hail/src/is/hail/utils/Py4jUtils.scala b/hail/hail/src/is/hail/utils/py4jutils.scala
similarity index 64%
rename from hail/hail/src/is/hail/utils/Py4jUtils.scala
rename to hail/hail/src/is/hail/utils/py4jutils.scala
index 3e3b08cad22..b76029fa5b4 100644
--- a/hail/hail/src/is/hail/utils/Py4jUtils.scala
+++ b/hail/hail/src/is/hail/utils/py4jutils.scala
@@ -1,8 +1,6 @@
 package is.hail.utils
 
-import is.hail.expr.JSONAnnotationImpex
 import is.hail.io.fs.{FS, FileListEntry, FileStatus, SeekableDataInputStream}
-import is.hail.types.virtual.Type
 
 import scala.jdk.CollectionConverters._
 
@@ -14,15 +12,11 @@ import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFact
 import org.json4s.JsonAST._
 import org.json4s.jackson.JsonMethods
 
-trait Py4jUtils extends Logging {
-  def arrayToArrayList[T](arr: Array[T]): java.util.ArrayList[T] = {
-    val list = new java.util.ArrayList[T]()
-    for (elem <- arr)
-      list.add(elem)
-    list
-  }
+object py4jutils extends Logging {
+  def pyHandleException(t: Throwable): (String, String, Int) =
+    handleForPython(t)
 
-  def iterableToArrayList[T](it: Iterable[T]): java.util.ArrayList[T] = {
+  def pyIterableToArrayList[T](it: Iterable[T]): java.util.ArrayList[T] = {
     val list = new java.util.ArrayList[T]()
     for (elem <- it)
       list.add(elem)
@@ -30,48 +24,27 @@ trait Py4jUtils extends Logging {
   }
 
   // we cannot construct an array because we don't have the class tag
-  def arrayListToISeq[T](al: java.util.ArrayList[T]): IndexedSeq[T] = al.asScala.toIndexedSeq
-
-  def arrayListToSet[T](al: java.util.ArrayList[T]): Set[T] = al.asScala.toSet
-
-  def javaMapToMap[K, V](jm: java.util.Map[K, V]): Map[K, V] = jm.asScala.toMap
-
-  def makeIndexedSeq[T](arr: Array[T]): IndexedSeq[T] = arr: IndexedSeq[T]
-
-  def makeInt(i: Int): Int = i
-
-  def makeInt(l: Long): Int = l.toInt
-
-  def makeLong(i: Int): Long = i.toLong
-
-  def makeLong(l: Long): Long = l
+  def pyArrayListToISeq[T](al: java.util.ArrayList[T]): IndexedSeq[T] =
+    al.asScala.toIndexedSeq
 
-  def makeFloat(f: Float): Float = f
-
-  def makeFloat(d: Double): Float = d.toFloat
-
-  def makeDouble(f: Float): Double = f.toDouble
-
-  def makeDouble(d: Double): Double = d
-
-  def ls(fs: FS, path: String): String = {
+  def pyLs(fs: FS, path: String): String = {
     val statuses = fs.listDirectory(path)
     JsonMethods.compact(JArray(statuses.map(fs => fileListEntryToJson(fs)).toList))
   }
 
-  def fileStatus(fs: FS, path: String): String = {
+  def pyFileStatus(fs: FS, path: String): String = {
     val stat = fs.fileStatus(path)
     JsonMethods.compact(fileStatusToJson(stat))
   }
 
-  def fileListEntry(fs: FS, path: String): String = {
+  def pyFileListEntry(fs: FS, path: String): String = {
     val stat = fs.fileListEntry(path)
     JsonMethods.compact(fileListEntryToJson(stat))
   }
 
-  private def fileStatusToJson(fs: FileStatus): JObject = {
+  private[this] def fileStatusToJson(fs: FileStatus): JObject =
     JObject(
-      "path" -> JString(fs.getPath.toString),
+      "path" -> JString(fs.getPath),
       "size" -> JInt(fs.getLen),
       "is_link" -> JBool(fs.isSymlink),
       "modification_time" ->
@@ -90,54 +63,32 @@ trait Py4jUtils extends Logging {
           JNull
       ),
     )
-  }
 
-  private def fileListEntryToJson(fs: FileListEntry): JObject =
+  private[this] def fileListEntryToJson(fs: FileListEntry): JObject =
     JObject(fileStatusToJson(fs).obj :+ ("is_dir" -> JBool(fs.isDirectory)))
 
-  private val kilo: Long = 1024
-  private val mega: Long = kilo * 1024
-  private val giga: Long = mega * 1024
-  private val tera: Long = giga * 1024
-
-  def readableBytes(bytes: Long): String = {
-    if (bytes < kilo)
-      bytes.toString
-    else if (bytes < mega)
-      formatDigits(bytes, kilo) + "K"
-    else if (bytes < giga)
-      formatDigits(bytes, mega) + "M"
-    else if (bytes < tera)
-      formatDigits(bytes, giga) + "G"
-    else
-      formatDigits(bytes, tera) + "T"
-  }
-
-  private def formatDigits(n: Long, factor: Long): String =
-    "%.1f".format(n / factor.toDouble)
-
-  def readFile(fs: FS, path: String, buffSize: Int): HadoopSeekablePyReader =
+  def pyReadFile(fs: FS, path: String, buffSize: Int): HadoopSeekablePyReader =
     new HadoopSeekablePyReader(fs.fileListEntry(path), fs.openNoCompression(path), buffSize)
 
-  def readFileCodec(fs: FS, path: String, buffSize: Int): HadoopPyReader =
+  def pyReadFileCodec(fs: FS, path: String, buffSize: Int): HadoopPyReader =
     new HadoopPyReader(fs.open(path), buffSize)
 
-  def writeFile(fs: FS, path: String, exclusive: Boolean): HadoopPyWriter = {
+  def pyWriteFile(fs: FS, path: String, exclusive: Boolean): HadoopPyWriter = {
     if (exclusive && fs.exists(path))
       fatal(s"a file already exists at '$path'")
     new HadoopPyWriter(fs.createNoCompression(path))
   }
 
-  def writeFileCodec(fs: FS, path: String, exclusive: Boolean): HadoopPyWriter = {
+  def pyWriteFileCodec(fs: FS, path: String, exclusive: Boolean): HadoopPyWriter = {
     if (exclusive && fs.exists(path))
       fatal(s"a file already exists at '$path'")
     new HadoopPyWriter(fs.create(path))
   }
 
-  val LogFormat: String =
+  private[this] val LogFormat: String =
     "%d{yyyy-MM-dd HH:mm:ss.SSS} %c{1}: %p: %m%n"
 
-  def configureLogging(logFile: String, quiet: Boolean, append: Boolean): Unit = {
+  def pyConfigureLogging(logFile: String, quiet: Boolean, append: Boolean): Unit = {
     val configBuilder =
       ConfigurationBuilderFactory
         .newConfigurationBuilder()
@@ -189,11 +140,6 @@ trait Py4jUtils extends Logging {
         .build(false)
     )
   }
-
-  def makeJSON(t: Type, value: Any): String = {
-    val jv = JSONAnnotationImpex.exportAnnotation(value, t)
-    JsonMethods.compact(jv)
-  }
 }
 
 class HadoopPyReader(in: InputStream, buffSize: Int) {
diff --git a/hail/hail/src/is/hail/utils/richUtils/Implicits.scala b/hail/hail/src/is/hail/utils/richUtils/Implicits.scala
deleted file mode 100644
index d38d74d5638..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/Implicits.scala
+++ /dev/null
@@ -1,146 +0,0 @@
-package is.hail.utils.richUtils
-
-import is.hail.annotations.{JoinedRegionValue, Region, RegionValue}
-import is.hail.asm4s.{Code, Value}
-import is.hail.io.{InputBuffer, OutputBuffer, RichContextRDDLong, RichContextRDDRegionValue}
-import is.hail.sparkextras._
-import is.hail.utils.{HailIterator, MultiArray2, Truncatable, WithContext}
-import is.hail.utils.compat.immutable.ArraySeq
-
-import scala.collection.compat._
-import scala.collection.mutable
-import scala.reflect.ClassTag
-import scala.util.matching.Regex
-
-import java.io.InputStream
-
-import breeze.linalg.DenseMatrix
-import org.apache.spark.SparkContext
-import org.apache.spark.mllib.linalg.distributed.IndexedRowMatrix
-import org.apache.spark.rdd.RDD
-import org.apache.spark.sql.Row
-
-trait Implicits {
-  implicit def toRichArray[T](a: Array[T]): RichArray[T] = new RichArray(a)
-
-  implicit def toRichArraySeqCompanion(a: ArraySeq.type): RichArraySeqCompanion.type =
-    RichArraySeqCompanion
-
-  implicit def toRichIndexedSeq[T](s: IndexedSeq[T]): RichIndexedSeq[T] = new RichIndexedSeq(s)
-
-  implicit def toRichIndexedSeqAnyRef[T <: AnyRef](s: IndexedSeq[T]): RichIndexedSeqAnyRef[T] =
-    new RichIndexedSeqAnyRef(s)
-
-  implicit def arrayToRichIndexedSeq[T](s: Array[T]): RichIndexedSeq[T] = new RichIndexedSeq(s)
-
-  implicit def toRichBoolean(b: Boolean): RichBoolean = new RichBoolean(b)
-
-  implicit def toRichDenseMatrixDouble(m: DenseMatrix[Double]): RichDenseMatrixDouble =
-    new RichDenseMatrixDouble(m)
-
-  implicit def toRichEnumeration[T <: Enumeration](e: T): RichEnumeration[T] =
-    new RichEnumeration(e)
-
-  implicit def toRichIndexedRowMatrix(irm: IndexedRowMatrix): RichIndexedRowMatrix =
-    new RichIndexedRowMatrix(irm)
-
-  implicit def toRichIterable[T](i: Iterable[T]): RichIterable[T] = new RichIterable(i)
-
-  implicit def toRichIterable[T](a: Array[T]): RichIterable[T] = new RichIterable(a)
-
-  implicit def toRichContextIterator[T](it: Iterator[WithContext[T]]): RichContextIterator[T] =
-    new RichContextIterator[T](it)
-
-  implicit def toRichIterator[T](it: Iterator[T]): RichIterator[T] = new RichIterator[T](it)
-
-  implicit def toRichIteratorLong(it: Iterator[Long]): RichIteratorLong = new RichIteratorLong(it)
-
-  implicit def toRichRowIterator(it: Iterator[Row]): RichRowIterator = new RichRowIterator(it)
-
-  implicit def toRichMap[K, V](m: Map[K, V]): RichMap[K, V] = new RichMap(m)
-
-  implicit def toRichMultiArray2Long(ma: MultiArray2[Long]): RichMultiArray2Long =
-    new RichMultiArray2Long(ma)
-
-  implicit def toRichMultiArray2Int(ma: MultiArray2[Int]): RichMultiArray2Int =
-    new RichMultiArray2Int(ma)
-
-  implicit def toRichMultiArray2Double(ma: MultiArray2[Double]): RichMultiArray2Double =
-    new RichMultiArray2Double(ma)
-
-  implicit def toRichMutableMap[K, V](m: mutable.Map[K, V]): RichMutableMap[K, V] =
-    new RichMutableMap(m)
-
-  implicit def toRichOption[T](o: Option[T]): RichOption[T] = new RichOption[T](o)
-
-  implicit def toRichOrderedArray[T: Ordering](a: Array[T]): RichOrderedArray[T] =
-    new RichOrderedArray(a)
-
-  implicit def toRichOrderedSeq[T: Ordering](s: Seq[T]): RichOrderedSeq[T] =
-    new RichOrderedSeq[T](s)
-
-  implicit def toRichPairRDD[K, V](r: RDD[(K, V)])(implicit kct: ClassTag[K], vct: ClassTag[V])
-    : RichPairRDD[K, V] = new RichPairRDD(r)
-
-  implicit def toRichPredicate[A](f: A => Boolean): RichPredicate[A] = new RichPredicate[A](f)
-
-  implicit def toRichRDD[T](r: RDD[T])(implicit tct: ClassTag[T]): RichRDD[T] = new RichRDD(r)
-
-  implicit def toRichContextRDDRegionValue(r: ContextRDD[RegionValue]): RichContextRDDRegionValue =
-    new RichContextRDDRegionValue(r)
-
-  implicit def toRichContextRDDLong(r: ContextRDD[Long]): RichContextRDDLong =
-    new RichContextRDDLong(r)
-
-  implicit def toRichRegex(r: Regex): RichRegex = new RichRegex(r)
-
-  implicit def toRichRow(r: Row): RichRow = new RichRow(r)
-
-  implicit def toRichSC(sc: SparkContext): RichSparkContext = new RichSparkContext(sc)
-
-  implicit def toRichString(str: String): RichString = new RichString(str)
-
-  implicit def toTruncatable(s: String): Truncatable = s.truncatable()
-
-  implicit def toTruncatable[T](it: Iterable[T]): Truncatable = it.truncatable()
-
-  implicit def toTruncatable(arr: Array[_]): Truncatable = toTruncatable(arr: Iterable[_])
-
-  implicit def toHailIteratorDouble(it: HailIterator[Int]): HailIterator[Double] =
-    new HailIterator[Double] {
-      override def next(): Double = it.next().toDouble
-      override def hasNext: Boolean = it.hasNext
-    }
-
-  implicit def toRichInputStream(in: InputStream): RichInputStream = new RichInputStream(in)
-
-  implicit def toRichJoinedRegionValue(jrv: JoinedRegionValue): RichJoinedRegionValue =
-    new RichJoinedRegionValue(jrv)
-
-  implicit def valueToRichCodeRegion(r: Value[Region]): RichCodeRegion = new RichCodeRegion(r)
-
-  implicit def toRichCodeRegion(r: Code[Region]): RichCodeRegion = new RichCodeRegion(r)
-
-  implicit def toRichPartialKleisliOptionFunction[A, B](x: PartialFunction[A, Option[B]])
-    : RichPartialKleisliOptionFunction[A, B] = new RichPartialKleisliOptionFunction(x)
-
-  implicit def toContextPairRDDFunctions[K: ClassTag, V: ClassTag](x: ContextRDD[(K, V)])
-    : ContextPairRDDFunctions[K, V] = new ContextPairRDDFunctions(x)
-
-  implicit def toRichContextRDD[T: ClassTag](x: ContextRDD[T]): RichContextRDD[T] =
-    new RichContextRDD(x)
-
-  implicit def toRichContextRDDRow(x: ContextRDD[Row]): RichContextRDDRow = new RichContextRDDRow(x)
-
-  implicit def valueToRichCodeInputBuffer(in: Value[InputBuffer]): RichCodeInputBuffer =
-    new RichCodeInputBuffer(in)
-
-  implicit def valueToRichCodeOutputBuffer(out: Value[OutputBuffer]): RichCodeOutputBuffer =
-    new RichCodeOutputBuffer(out)
-
-  implicit def toRichCodeIterator[T](it: Code[Iterator[T]]): RichCodeIterator[T] =
-    new RichCodeIterator[T](it)
-
-  implicit def valueToRichCodeIterator[T](it: Value[Iterator[T]]): RichCodeIterator[T] =
-    new RichCodeIterator[T](it)
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichArray.scala b/hail/hail/src/is/hail/utils/richUtils/RichArray.scala
deleted file mode 100644
index 7f3d93760d0..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichArray.scala
+++ /dev/null
@@ -1,38 +0,0 @@
-package is.hail.utils.richUtils
-
-import is.hail.io.{DoubleInputBuffer, DoubleOutputBuffer}
-import is.hail.io.fs.FS
-import is.hail.utils._
-
-object RichArray {
-  val defaultBufSize: Int = 4096 << 3
-
-  def importFromDoubles(fs: FS, path: String, n: Int): Array[Double] = {
-    val a = new Array[Double](n)
-    importFromDoubles(fs, path, a, defaultBufSize)
-    a
-  }
-
-  def importFromDoubles(fs: FS, path: String, a: Array[Double], bufSize: Int): Unit =
-    using(fs.open(path)) { is =>
-      val in = new DoubleInputBuffer(is, bufSize)
-
-      in.readDoubles(a)
-    }
-
-  def exportToDoubles(fs: FS, path: String, a: Array[Double]): Unit =
-    exportToDoubles(fs, path, a, defaultBufSize)
-
-  def exportToDoubles(fs: FS, path: String, a: Array[Double], bufSize: Int): Unit = {
-    using(fs.create(path)) { os =>
-      val out = new DoubleOutputBuffer(os, bufSize)
-
-      out.writeDoubles(a)
-      out.flush()
-    }
-  }
-}
-
-class RichArray[T](val a: Array[T]) extends AnyVal {
-  def index: Map[T, Int] = a.zipWithIndex.toMap
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichEnumeration.scala b/hail/hail/src/is/hail/utils/richUtils/RichEnumeration.scala
deleted file mode 100644
index e373a9940d6..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichEnumeration.scala
+++ /dev/null
@@ -1,6 +0,0 @@
-package is.hail.utils.richUtils
-
-class RichEnumeration[T <: Enumeration](val e: T) extends AnyVal {
-  def withNameOption(name: String): Option[T#Value] =
-    e.values.find(_.toString == name)
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichInputStream.scala b/hail/hail/src/is/hail/utils/richUtils/RichInputStream.scala
deleted file mode 100644
index 61b5ab8f34f..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichInputStream.scala
+++ /dev/null
@@ -1,31 +0,0 @@
-package is.hail.utils.richUtils
-
-import is.hail.utils._
-
-import java.io.InputStream
-
-class RichInputStream(val in: InputStream) extends AnyVal {
-  def readFully(to: Array[Byte]): Unit =
-    readFully(to, 0, to.length)
-
-  def readFully(to: Array[Byte], toOff: Int, n: Int): Unit = {
-    val nRead = readRepeatedly(to, toOff, n)
-    if (nRead < n) fatal(s"Premature end of file: expected $n bytes, found $nRead")
-  }
-
-  def readRepeatedly(to: Array[Byte], toOff: Int, n: Int): Int = {
-    assert(toOff + n <= to.length)
-    var read = 0
-    var endOfStream = false
-    while (read < n && !endOfStream) {
-      val r = in.read(to, toOff + read, n - read)
-      if (r < 0)
-        endOfStream = true
-      else
-        read += r
-    }
-    read
-  }
-
-  def readRepeatedly(to: Array[Byte]): Int = readRepeatedly(to, 0, to.length)
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichMultiArray2Numeric.scala b/hail/hail/src/is/hail/utils/richUtils/RichMultiArray2Numeric.scala
deleted file mode 100644
index 44ec8eb203a..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichMultiArray2Numeric.scala
+++ /dev/null
@@ -1,84 +0,0 @@
-package is.hail.utils.richUtils
-
-import is.hail.utils.MultiArray2
-
-class RichMultiArray2Long(val ma: MultiArray2[Long]) extends AnyVal {
-
-  def addElementWise(other: MultiArray2[Long]): MultiArray2[Long] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) += arr2(i)
-      i += 1
-    }
-    ma
-  }
-
-  def multiplyElementWise(other: MultiArray2[Long]): MultiArray2[Long] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) *= arr2(i)
-      i += 1
-    }
-    ma
-  }
-}
-
-class RichMultiArray2Double(val ma: MultiArray2[Double]) extends AnyVal {
-
-  def addElementWise(other: MultiArray2[Double]): MultiArray2[Double] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) += arr2(i)
-      i += 1
-    }
-    ma
-  }
-
-  def multiplyElementWise(other: MultiArray2[Double]): MultiArray2[Double] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) *= arr2(i)
-      i += 1
-    }
-    ma
-  }
-}
-
-class RichMultiArray2Int(val ma: MultiArray2[Int]) extends AnyVal {
-
-  def addElementWise(other: MultiArray2[Int]): MultiArray2[Int] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) += arr2(i)
-      i += 1
-    }
-    ma
-  }
-
-  def multiplyElementWise(other: MultiArray2[Int]): MultiArray2[Int] = {
-    require(ma.n1 == other.n1 && ma.n2 == other.n2)
-    val arr1 = ma.array
-    val arr2 = other.array
-    var i = 0
-    while (i < arr1.length) {
-      arr1(i) *= arr2(i)
-      i += 1
-    }
-    ma
-  }
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichRegex.scala b/hail/hail/src/is/hail/utils/richUtils/RichRegex.scala
deleted file mode 100644
index 1a2f0b2f006..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichRegex.scala
+++ /dev/null
@@ -1,7 +0,0 @@
-package is.hail.utils.richUtils
-
-import scala.util.matching.Regex
-
-class RichRegex(r: Regex) {
-  def matches(s: String): Boolean = r.pattern.matcher(s).matches()
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichSparkContext.scala b/hail/hail/src/is/hail/utils/richUtils/RichSparkContext.scala
deleted file mode 100644
index 64856109dac..00000000000
--- a/hail/hail/src/is/hail/utils/richUtils/RichSparkContext.scala
+++ /dev/null
@@ -1,30 +0,0 @@
-package is.hail.utils.richUtils
-
-import is.hail.utils._
-
-import org.apache.spark.SparkContext
-import org.apache.spark.rdd.RDD
-
-class RichSparkContext(val sc: SparkContext) extends AnyVal {
-  def textFilesLines(files: Array[String], nPartitions: Int = sc.defaultMinPartitions)
-    : RDD[WithContext[String]] = {
-
-    /* Don't use:
-     * sc.union(files.map(sc.textFile, nPartitions)) since it asks for nPartitions per file instead
-     * of nPartitions over all. */
-    val rdd = sc.textFile(files.mkString(","), nPartitions)
-    val partitionFile = rdd.partitions.map(partitionPath)
-
-    rdd
-      .mapPartitionsWithIndex { case (i, it) =>
-        // FIXME subclass TextInputFormat to return (file, line)
-        val file = partitionFile(i)
-        it.map(line => WithContext(line, Context(line, file, None)))
-      }
-  }
-
-  def textFileLines(file: String, nPartitions: Int = sc.defaultMinPartitions)
-    : RDD[WithContext[String]] =
-    sc.textFile(file, nPartitions)
-      .map(l => WithContext(l, Context(l, file, None)))
-}
diff --git a/hail/hail/src/is/hail/variant/Call.scala b/hail/hail/src/is/hail/variant/Call.scala
index 1faede6d86f..3509b23e925 100644
--- a/hail/hail/src/is/hail/variant/Call.scala
+++ b/hail/hail/src/is/hail/variant/Call.scala
@@ -1,7 +1,9 @@
 package is.hail.variant
 
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.Parser
 import is.hail.utils._
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.annotation.switch
 import scala.jdk.CollectionConverters._
@@ -444,9 +446,9 @@ object Call extends Serializable {
     }
 
     new IndexedSeq[Int] with Serializable {
-      def length: Int = nAlleles
+      override def length: Int = nAlleles
 
-      def apply(idx: Int): Int = {
+      override def apply(idx: Int): Int = {
         if (idx < 0 || idx >= nAlleles)
           throw new ArrayIndexOutOfBoundsException(idx)
 
diff --git a/hail/hail/src/is/hail/variant/ReferenceGenome.scala b/hail/hail/src/is/hail/variant/ReferenceGenome.scala
index 2b390ca6977..69622bea704 100644
--- a/hail/hail/src/is/hail/variant/ReferenceGenome.scala
+++ b/hail/hail/src/is/hail/variant/ReferenceGenome.scala
@@ -2,6 +2,8 @@ package is.hail.variant
 
 import is.hail.annotations.ExtendedOrdering
 import is.hail.backend.ExecuteContext
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.{toRichIndexedSeq, toRichIterable}
 import is.hail.expr.{
   JSONExtractContig, JSONExtractIntervalLocus, JSONExtractReferenceGenome, Parser,
 }
@@ -13,7 +15,6 @@ import is.hail.io.reference.{
 import is.hail.types._
 import is.hail.types.virtual.{TLocus, Type}
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 import scala.jdk.CollectionConverters._
@@ -108,7 +109,8 @@ case class ReferenceGenome(
   val locusOrdering = {
     val localContigsIndex = contigsIndex
     new Ordering[Locus] {
-      def compare(x: Locus, y: Locus): Int = ReferenceGenome.compare(localContigsIndex, x, y)
+      override def compare(x: Locus, y: Locus): Int =
+        ReferenceGenome.compare(localContigsIndex, x, y)
     }
   }
 
@@ -496,12 +498,12 @@ object ReferenceGenome {
   }
 
   def read(is: InputStream): ReferenceGenome = {
-    implicit val formats = defaultJSONFormats
+    implicit val formats = DefaultFormats
     JsonMethods.parse(is).extract[JSONExtractReferenceGenome].toReferenceGenome
   }
 
   def parse(str: String): ReferenceGenome = {
-    implicit val formats = defaultJSONFormats
+    implicit val formats = DefaultFormats
     JsonMethods.parse(str).extract[JSONExtractReferenceGenome].toReferenceGenome
   }
 
diff --git a/hail/hail/src/is/hail/variant/RegionValueVariant.scala b/hail/hail/src/is/hail/variant/RegionValueVariant.scala
index fe223effb09..2702a2bb0cd 100644
--- a/hail/hail/src/is/hail/variant/RegionValueVariant.scala
+++ b/hail/hail/src/is/hail/variant/RegionValueVariant.scala
@@ -17,7 +17,7 @@ class RegionValueVariant(rowType: PStruct) extends View {
   private var cachedAlleles: Array[String] = null
   private var cachedLocus: Locus = null
 
-  def set(address: Long): Unit = {
+  override def set(address: Long): Unit = {
     if (!rowType.isFieldDefined(address, locusIdx))
       fatal(s"The row field 'locus' cannot have missing values.")
     if (!rowType.isFieldDefined(address, allelesIdx))
diff --git a/hail/hail/test/src/is/hail/HailSuite.scala b/hail/hail/test/src/is/hail/HailSuite.scala
index d2365c19d31..37031aeda35 100644
--- a/hail/hail/test/src/is/hail/HailSuite.scala
+++ b/hail/hail/test/src/is/hail/HailSuite.scala
@@ -5,6 +5,8 @@ import is.hail.annotations._
 import is.hail.asm4s.HailClassLoader
 import is.hail.backend.{Backend, ExecuteContext, OwningTempFileManager}
 import is.hail.backend.spark.SparkBackend
+import is.hail.collection.{FastSeq, ImmutableMap}
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.expr.ir.functions.IRFunctionRegistry
diff --git a/hail/hail/test/src/is/hail/TestUtils.scala b/hail/hail/test/src/is/hail/TestUtils.scala
index 4abfa976a34..3efd44ed59f 100644
--- a/hail/hail/test/src/is/hail/TestUtils.scala
+++ b/hail/hail/test/src/is/hail/TestUtils.scala
@@ -1,8 +1,10 @@
 package is.hail
 
 import is.hail.annotations.{Region, RegionPool, RegionValueBuilder, SafeRow}
-import is.hail.asm4s._
+import is.hail.asm4s.{implicits => _, _}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.{
   freshName, streamAggIR, BindingEnv, Env, IR, Interpret, MapIR, MatrixIR, MatrixRead, Name,
   SingleCodeEmitParamType, Subst,
@@ -16,7 +18,6 @@ import is.hail.types.physical.{PBaseStruct, PCanonicalArray, PType}
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
 import is.hail.types.virtual._
 import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 import is.hail.variant._
 
 import java.io.PrintWriter
diff --git a/hail/hail/test/src/is/hail/annotations/RegionSuite.scala b/hail/hail/test/src/is/hail/annotations/RegionSuite.scala
index 889839f1bc4..2b1590e0632 100644
--- a/hail/hail/test/src/is/hail/annotations/RegionSuite.scala
+++ b/hail/hail/test/src/is/hail/annotations/RegionSuite.scala
@@ -1,6 +1,6 @@
 package is.hail.annotations
 
-import is.hail.expr.ir.LongArrayBuilder
+import is.hail.collection.LongArrayBuilder
 import is.hail.utils.using
 
 import scala.collection.mutable.ArrayBuffer
diff --git a/hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala b/hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala
index 86323056c85..cd720005def 100644
--- a/hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala
+++ b/hail/hail/test/src/is/hail/annotations/StagedConstructorSuite.scala
@@ -3,6 +3,7 @@ package is.hail.annotations
 import is.hail.HailSuite
 import is.hail.asm4s._
 import is.hail.backend.{ExecuteContext, HailTaskContext}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCode, EmitFunctionBuilder, IEmitCode, RequirednessSuite}
 import is.hail.io.fs.FS
 import is.hail.scalacheck._
diff --git a/hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala b/hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala
index ff9da3c7309..38f5d7c9c08 100644
--- a/hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala
+++ b/hail/hail/test/src/is/hail/annotations/UnsafeSuite.scala
@@ -2,12 +2,12 @@ package is.hail.annotations
 
 import is.hail.HailSuite
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.io._
 import is.hail.rvd.AbstractRVDSpec
 import is.hail.scalacheck._
 import is.hail.types.physical._
 import is.hail.types.virtual.{TArray, TStruct, Type}
-import is.hail.utils._
 
 import scala.util.Random
 
diff --git a/hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala b/hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala
index 7efe5aff9d8..2b6195f3815 100644
--- a/hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala
+++ b/hail/hail/test/src/is/hail/asm4s/ASM4SSuite.scala
@@ -2,7 +2,7 @@ package is.hail.asm4s
 
 import is.hail.HailSuite
 import is.hail.asm4s.Code._
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import scala.language.postfixOps
 
diff --git a/hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala b/hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala
index e4a54c45a9d..d490b7add20 100644
--- a/hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala
+++ b/hail/hail/test/src/is/hail/backend/ServiceBackendSuite.scala
@@ -2,9 +2,10 @@ package is.hail.backend
 
 import is.hail.HailSuite
 import is.hail.backend.service.{BatchJobConfig, ServiceBackend, WireProtocol}
+import is.hail.collection.FastSeq
 import is.hail.services._
 import is.hail.services.JobGroupStates.{Cancelled, Failure, Success}
-import is.hail.utils.{handleForPython, tokenUrlSafe, using, FastSeq, HailWorkerException}
+import is.hail.utils.{handleForPython, tokenUrlSafe, using, HailWorkerException}
 
 import scala.collection.compat.immutable.LazyList
 import scala.concurrent.CancellationException
@@ -241,6 +242,8 @@ class ServiceBackendSuite extends HailSuite with IdiomaticMockito with OptionVal
           regions = Array("lunar1"),
         )
 
+      // no idea why this trigger the missing override rule
+      @SuppressWarnings(Array("org.wartremover.contrib.warts.MissingOverride"))
       val batchClient =
         mock[BatchClient]
 
diff --git a/hail/hail/test/src/is/hail/utils/ArrayBuilderSuite.scala b/hail/hail/test/src/is/hail/collection/ArrayBuilderSuite.scala
similarity index 94%
rename from hail/hail/test/src/is/hail/utils/ArrayBuilderSuite.scala
rename to hail/hail/test/src/is/hail/collection/ArrayBuilderSuite.scala
index 42b6166f79f..1b2dcc0a2ef 100644
--- a/hail/hail/test/src/is/hail/utils/ArrayBuilderSuite.scala
+++ b/hail/hail/test/src/is/hail/collection/ArrayBuilderSuite.scala
@@ -1,6 +1,4 @@
-package is.hail.utils
-
-import is.hail.expr.ir.IntArrayBuilder
+package is.hail.collection
 
 import org.scalatestplus.testng.TestNGSuite
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/utils/ArrayStackSuite.scala b/hail/hail/test/src/is/hail/collection/ArrayStackSuite.scala
similarity index 97%
rename from hail/hail/test/src/is/hail/utils/ArrayStackSuite.scala
rename to hail/hail/test/src/is/hail/collection/ArrayStackSuite.scala
index 593b21ecc56..0a674e50068 100644
--- a/hail/hail/test/src/is/hail/utils/ArrayStackSuite.scala
+++ b/hail/hail/test/src/is/hail/collection/ArrayStackSuite.scala
@@ -1,4 +1,4 @@
-package is.hail.utils
+package is.hail.collection
 
 import org.scalatestplus.testng.TestNGSuite
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/utils/BinaryHeapSuite.scala b/hail/hail/test/src/is/hail/collection/BinaryHeapSuite.scala
similarity index 99%
rename from hail/hail/test/src/is/hail/utils/BinaryHeapSuite.scala
rename to hail/hail/test/src/is/hail/collection/BinaryHeapSuite.scala
index 90d4610642e..88601306abe 100644
--- a/hail/hail/test/src/is/hail/utils/BinaryHeapSuite.scala
+++ b/hail/hail/test/src/is/hail/collection/BinaryHeapSuite.scala
@@ -1,4 +1,4 @@
-package is.hail.utils
+package is.hail.collection
 
 import is.hail.scalacheck._
 
diff --git a/hail/hail/test/src/is/hail/utils/FlipbookIteratorSuite.scala b/hail/hail/test/src/is/hail/collection/FlipbookIteratorSuite.scala
similarity index 94%
rename from hail/hail/test/src/is/hail/utils/FlipbookIteratorSuite.scala
rename to hail/hail/test/src/is/hail/collection/FlipbookIteratorSuite.scala
index eca7c01483c..5c8de2edd6e 100644
--- a/hail/hail/test/src/is/hail/utils/FlipbookIteratorSuite.scala
+++ b/hail/hail/test/src/is/hail/collection/FlipbookIteratorSuite.scala
@@ -1,7 +1,9 @@
-package is.hail.utils
+package is.hail.collection
 
 import is.hail.HailSuite
-import is.hail.utils.compat.mutable.{Growable, GrowableCompat}
+import is.hail.collection.compat.mutable.{Growable, GrowableCompat}
+import is.hail.collection.implicits.toRichIterator
+import is.hail.utils.{Muple, OrderingView}
 
 import scala.collection.mutable.ArrayBuffer
 import scala.reflect.runtime.universe._
@@ -34,10 +36,10 @@ class FlipbookIteratorSuite extends HailSuite {
   def boxOrdView[A: Ordering]: OrderingView[Box[A]] = new OrderingView[Box[A]] {
     var value: A = _
 
-    def setFiniteValue(a: Box[A]): Unit =
+    override def setFiniteValue(a: Box[A]): Unit =
       value = a.value
 
-    def compareFinite(a: Box[A]): Int =
+    override def compareFinite(a: Box[A]): Int =
       implicitly[Ordering[A]].compare(value, a.value)
   }
 
@@ -48,18 +50,18 @@ class FlipbookIteratorSuite extends HailSuite {
 
       override def knownSize: Int = buf.size
 
-      def clear(): Unit = buf.clear()
+      override def clear(): Unit = buf.clear()
 
-      def addOne(x: Box[A]) = {
+      override def addOne(x: Box[A]) = {
         buf += x.value
         this
       }
 
-      def iterator: Iterator[Box[A]] = new Iterator[Box[A]] {
+      override def iterator: Iterator[Box[A]] = new Iterator[Box[A]] {
         var i = 0
-        def hasNext = i < buf.size
+        override def hasNext = i < buf.size
 
-        def next() = {
+        override def next() = {
           box.value = buf(i)
           i += 1
           box
@@ -79,7 +81,7 @@ class FlipbookIteratorSuite extends HailSuite {
     val sm = new StateMachine[Box[A]] {
       val value: Box[A] = Box[A]
       var isValid = true
-      def advance(): Unit =
+      override def advance(): Unit =
         if (it.hasNext)
           value.value = it.next()
         else
diff --git a/hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala b/hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala
index bb5d7cfbf27..27c565241fa 100644
--- a/hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/Aggregators2Suite.scala
@@ -3,6 +3,8 @@ package is.hail.expr.ir
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.agg._
 import is.hail.expr.ir.compile.CompileWithAggregators
 import is.hail.expr.ir.defs._
@@ -11,7 +13,6 @@ import is.hail.types.VirtualTypeWithReq
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.PTypeReferenceSingleCodeType
 import is.hail.types.virtual._
-import is.hail.utils._
 import is.hail.variant.{Call0, Call1, Call2}
 
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala
index 438b5d37364..993701ba7da 100644
--- a/hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/AggregatorsSuite.scala
@@ -2,6 +2,8 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.DeprecatedIRBuilder._
 import is.hail.expr.ir.defs.{
   AggFilter, AggGroupBy, ApplyAggOp, ApplyBinaryPrimOp, ArrayRef, Cast, GetField, I32, InsertFields,
@@ -10,7 +12,6 @@ import is.hail.expr.ir.defs.{
 }
 import is.hail.expr.ir.lowering.{DArrayLowering, LowerTableIR}
 import is.hail.types.virtual._
-import is.hail.utils.{toRichIterable, FastSeq}
 import is.hail.variant.Call2
 
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala
index e2105c355a7..a884003209d 100644
--- a/hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/ArrayDeforestationSuite.scala
@@ -1,10 +1,10 @@
 package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{
   GetField, GetTupleElement, If, MakeStruct, MakeTuple, StreamRange, ToArray, ToStream,
 }
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala
index 5119614127b..891c25273d6 100644
--- a/hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/ArrayFunctionsSuite.scala
@@ -2,10 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs.{ArraySlice, F32, F64, I32, In, MakeArray, NA, Str}
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.{DataProvider, Test}
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala
index a4728d6bb99..c6db566167c 100644
--- a/hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/BlockMatrixIRSuite.scala
@@ -2,6 +2,8 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs.{
   Apply, ApplyBinaryPrimOp, ApplyUnaryPrimOp, BlockMatrixWrite, ErrorIDs, F64, I64, Literal,
@@ -11,7 +13,6 @@ import is.hail.io.TypedCodecSpec
 import is.hail.linalg.BlockMatrix
 import is.hail.types.encoded.{EBlockMatrixNDArray, EFloat64Required}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 import java.lang.Math.floorDiv
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala
index fb0c9f540be..54ca2648b2b 100644
--- a/hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/DictFunctionsSuite.scala
@@ -2,10 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs.{NA, ToSet, ToStream}
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.{DataProvider, Test}
diff --git a/hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala b/hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala
index 9442e3bf9cd..2bb722cb11f 100644
--- a/hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/DistinctlyKeyedSuite.scala
@@ -1,11 +1,11 @@
 package is.hail.expr.ir
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{
   ApplyComparisonOp, GetField, I32, If, InsertFields, MakeStruct, Ref, StreamRange, TableCollect,
   TableWrite, ToArray,
 }
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.Test
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala b/hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala
index 917cac3350d..1a9193a3f29 100644
--- a/hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/EmitStreamSuite.scala
@@ -4,6 +4,8 @@ import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.annotations.{Region, SafeRow, ScalaToRegionValue}
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.agg.{CollectStateSig, PhysicalAggSig, TypedStateSig}
 import is.hail.expr.ir.compile.Compile
 import is.hail.expr.ir.defs._
@@ -120,7 +122,7 @@ class EmitStreamSuite extends HailSuite {
         var _eltRegion: Region = _
         var eos: Boolean = _
 
-        def init(outerRegion: Region, eltRegion: Region): Unit = _eltRegion = eltRegion
+        override def init(outerRegion: Region, eltRegion: Region): Unit = _eltRegion = eltRegion
 
         override def next(): Long =
           if (eos || !it.hasNext) {
diff --git a/hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
index ab6ab3843c2..499ac6d71ae 100644
--- a/hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/ExtractIntervalFiltersSuite.scala
@@ -1,10 +1,11 @@
 package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs._
 import is.hail.rvd.RVDPartitioner
 import is.hail.types.virtual._
-import is.hail.utils.{FastSeq, Interval, IntervalEndpoint}
+import is.hail.utils.{Interval, IntervalEndpoint}
 import is.hail.variant.{Locus, ReferenceGenome}
 
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala
index 39aea0108b3..2e11c8c32ea 100644
--- a/hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/FoldConstantsSuite.scala
@@ -1,17 +1,22 @@
 package is.hail.expr.ir
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{
-  AggLet, ApplyAggOp, ApplyScanOp, ApplySeeded, F64, I32, I64, RNGStateLiteral, Str,
+  AggLet, Apply, ApplyAggOp, ApplyScanOp, F64, I32, I64, RNGSplitStatic, RNGStateLiteral, Str,
 }
 import is.hail.types.virtual.{TFloat64, TInt32}
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.{DataProvider, Test}
 
 class FoldConstantsSuite extends HailSuite {
   @Test def testRandomBlocksFolding(): Unit = {
-    val x = ApplySeeded("rand_norm", FastSeq(F64(0d), F64(0d)), RNGStateLiteral(), 0L, TFloat64)
+    val x = Apply(
+      "rand_norm",
+      FastSeq.empty,
+      FastSeq(RNGSplitStatic(RNGStateLiteral(), 0L), F64(0d), F64(0d)),
+      TFloat64,
+    )
     assert(FoldConstants(ctx, x) == x)
   }
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala
index 86f3c9df62a..28a563066c3 100644
--- a/hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/ForwardLetsSuite.scala
@@ -2,10 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.HailSuite
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.defs._
 import is.hail.types.virtual._
-import is.hail.utils._
 
 import org.testng.annotations.{BeforeMethod, DataProvider, Test}
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala b/hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala
index 6581a4c99a0..d6289968f29 100644
--- a/hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/FunctionSuite.scala
@@ -3,11 +3,11 @@ package is.hail.expr.ir
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{ApplyBinaryPrimOp, I32, In}
 import is.hail.expr.ir.functions.{IRFunctionRegistry, RegistryFunctions}
 import is.hail.types.physical.stypes.interfaces._
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 import is.hail.variant.Call2
 
 import org.testng.annotations.Test
@@ -25,7 +25,7 @@ class ScalaTestCompanion {
 }
 
 object TestRegisterFunctions extends RegistryFunctions {
-  def registerAll(): Unit = {
+  override def registerAll(): Unit = {
     registerIR1("addone", TInt32, TInt32)((_, a, _) => ApplyBinaryPrimOp(Add(), a, I32(1)))
     registerJavaStaticFunction("compare", Array(TInt32, TInt32), TInt32, null)(
       classOf[java.lang.Integer],
@@ -82,22 +82,22 @@ class FunctionSuite extends HailSuite {
 
   @Test
   def testVariableUnification(): Unit = {
-    assert(IRFunctionRegistry.lookupUnseeded(
+    assert(IRFunctionRegistry.lookup(
       "testCodeUnification",
       TInt32,
       Seq(TInt32, TInt32),
     ).isDefined)
-    assert(IRFunctionRegistry.lookupUnseeded(
+    assert(IRFunctionRegistry.lookup(
       "testCodeUnification",
       TInt32,
       Seq(TInt64, TInt32),
     ).isEmpty)
-    assert(IRFunctionRegistry.lookupUnseeded(
+    assert(IRFunctionRegistry.lookup(
       "testCodeUnification",
       TInt64,
       Seq(TInt32, TInt32),
     ).isEmpty)
-    assert(IRFunctionRegistry.lookupUnseeded(
+    assert(IRFunctionRegistry.lookup(
       "testCodeUnification2",
       TArray(TInt32),
       Seq(TArray(TInt32)),
diff --git a/hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala
index da3628085ec..a4b0c7ffd20 100644
--- a/hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/GenotypeFunctionsSuite.scala
@@ -2,9 +2,9 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TestUtils._
 import is.hail.types.virtual.TFloat64
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.{DataProvider, Test}
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/IRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/IRSuite.scala
index eb70ae0a9d0..18298c408e7 100644
--- a/hail/hail/test/src/is/hail/expr/ir/IRSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/IRSuite.scala
@@ -4,6 +4,9 @@ import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.annotations.{BroadcastRow, ExtendedOrdering, SafeNDArray}
 import is.hail.backend.ExecuteContext
+import is.hail.collection.{FastSeq, IntArrayBuilder}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.Nat
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.agg._
@@ -21,7 +24,7 @@ import is.hail.types.physical.stypes._
 import is.hail.types.physical.stypes.primitives.SInt32
 import is.hail.types.virtual._
 import is.hail.types.virtual.TIterable.elementType
-import is.hail.utils.{FastSeq, _}
+import is.hail.utils._
 import is.hail.variant.{Call2, Locus}
 
 import scala.collection.compat._
@@ -39,19 +42,18 @@ class IRSuite extends HailSuite {
   @Test def testRandDifferentLengthUIDStrings(): Unit = {
     implicit val execStrats = ExecStrategy.lowering
     val staticUID: Long = 112233
-    var rng: IR = RNGStateLiteral()
-    rng = RNGSplit(rng, I64(12345))
+    var rng = RNGSplit(RNGSplitStatic(RNGStateLiteral(), staticUID), I64(12345))
     val expected1 = Threefry.pmac(ctx.rngNonce, staticUID, Array(12345L))
-    assertEvalsTo(ApplySeeded("rand_int64", IndexedSeq(), rng, staticUID, TInt64), expected1(0))
+    assertEvalsTo(Apply("rand_int64", ArraySeq.empty, ArraySeq(rng), TInt64), expected1(0))
 
     rng = RNGSplit(rng, I64(0))
     val expected2 = Threefry.pmac(ctx.rngNonce, staticUID, Array(12345L, 0L))
-    assertEvalsTo(ApplySeeded("rand_int64", IndexedSeq(), rng, staticUID, TInt64), expected2(0))
+    assertEvalsTo(Apply("rand_int64", ArraySeq.empty, ArraySeq(rng), TInt64), expected2(0))
 
     rng = RNGSplit(rng, I64(0))
     rng = RNGSplit(rng, I64(0))
     val expected3 = Threefry.pmac(ctx.rngNonce, staticUID, Array(12345L, 0L, 0L, 0L))
-    assertEvalsTo(ApplySeeded("rand_int64", IndexedSeq(), rng, staticUID, TInt64), expected3(0))
+    assertEvalsTo(Apply("rand_int64", ArraySeq.empty, ArraySeq(rng), TInt64), expected3(0))
     assert(expected1 != expected2)
     assert(expected2 != expected3)
     assert(expected1 != expected3)
@@ -3429,6 +3431,15 @@ class IRSuite extends HailSuite {
       },
       forIR(st)(_ => Void()) -> Array(st),
       streamAggIR(st)(x => ApplyAggOp(Sum())(Cast(x, TInt64))) -> Array(st),
+      StreamBufferedAggregate(
+        st,
+        Void(),
+        MakeStruct(ArraySeq("l" -> l)),
+        Void(),
+        l.name,
+        ArraySeq(pCollectSig),
+        27,
+      ) -> Array(st),
       streamAggScanIR(st)(x => ApplyScanOp(Sum())(Cast(x, TInt64))) -> Array(st),
       RunAgg(
         Begin(FastSeq(
@@ -4428,11 +4439,11 @@ class IRSuite extends HailSuite {
       assert(interval1.isDisjointFrom(kord, interval2))
     }
 
-    val splitterValueDuplicated = splitters.counter().mapValues(_ > 1)
+    val splitterValueCounts = splitters.counter()
     val intBuilder = new IntArrayBuilder()
     splitters.toSet.toIndexedSeq.sorted.foreach { e =>
       intBuilder.add(e)
-      if (splitterValueDuplicated(e)) {
+      if (splitterValueCounts(e) > 1) {
         intBuilder.add(e)
       }
     }
diff --git a/hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala b/hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala
index 0263f666260..b1ad7d47c4f 100644
--- a/hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/IntervalSuite.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{
   ErrorIDs, False, GetTupleElement, I32, If, Literal, MakeTuple, NA, True,
 }
diff --git a/hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala
index 5e7a17353dd..5eba97863e0 100644
--- a/hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/LiftLiteralsSuite.scala
@@ -2,9 +2,9 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{ApplyBinaryPrimOp, I64, MakeStruct, TableCount, TableGetGlobals}
 import is.hail.expr.ir.lowering.ExecuteRelational
-import is.hail.utils.FastSeq
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala
index 0ca00b8825f..33d9d89448e 100644
--- a/hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/LocusFunctionsSuite.scala
@@ -2,9 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{Apply, ErrorIDs, False, I32, I64, MakeArray, MakeTuple, NA, Str, True}
 import is.hail.types.virtual._
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.utils.Interval
 import is.hail.variant.{Locus, ReferenceGenome}
 
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala
index c2926463c4a..0891a2a35dd 100644
--- a/hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/MatrixIRSuite.scala
@@ -3,11 +3,13 @@ package is.hail.expr.ir
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.annotations.BroadcastRow
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.{toRichIterable, toRichOrderedArray}
 import is.hail.expr.JSONAnnotationImpex
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs.{
-  ApplySeeded, GetField, I32, InsertFields, MakeTuple, MatrixMultiWrite, MatrixWrite, RNGSplit,
-  RNGStateLiteral, Ref, TableCollect,
+  Apply, GetField, I32, InsertFields, MakeTuple, MatrixMultiWrite, MatrixWrite, RNGSplit,
+  RNGSplitStatic, RNGStateLiteral, Ref, TableCollect,
 }
 import is.hail.types.virtual._
 import is.hail.utils._
@@ -342,7 +344,7 @@ class MatrixIRSuite extends HailSuite {
   @Test def testMatrixFiltersWorkWithRandomness(): Unit = {
     val range = rangeMatrix(20, 20, Some(4), uids = true)
     def rand(rng: IR): IR =
-      ApplySeeded("rand_bool", FastSeq(0.5), rng, 0, TBoolean)
+      Apply("rand_bool", FastSeq.empty, FastSeq(RNGSplitStatic(rng, 0), 0.5), TBoolean)
 
     val colUID = GetField(Ref(MatrixIR.colName, range.typ.colType), MatrixReader.colUIDFieldName)
     val colRNG = RNGSplit(RNGStateLiteral(), colUID)
diff --git a/hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala
index a80f4112106..a7b9f3a56da 100644
--- a/hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/MemoryLeakSuite.scala
@@ -1,6 +1,8 @@
 package is.hail.expr.ir
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir
 import is.hail.expr.ir.defs.{Literal, ToArray, ToStream}
 import is.hail.types.virtual.{TArray, TBoolean, TSet, TString}
diff --git a/hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala b/hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala
index fa81fa53108..fad2aac8cf4 100644
--- a/hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/MissingArrayBuilderSuite.scala
@@ -1,7 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.asm4s.AsmFunction2
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import scala.reflect.ClassTag
 
@@ -11,7 +11,7 @@ import org.testng.annotations.{DataProvider, Test}
 class MissingArrayBuilderSuite extends TestNGSuite {
   def ordering[T <: AnyVal](f: (T, T) => Boolean): AsmFunction2[T, T, Boolean] =
     new AsmFunction2[T, T, Boolean] {
-      def apply(i: T, j: T): Boolean = f(i, j)
+      override def apply(i: T, j: T): Boolean = f(i, j)
     }
 
   def addToArrayBuilder[B <: MissingArrayBuilder, T](
diff --git a/hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala b/hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala
index 459e4337c85..75f3c2ed4a3 100644
--- a/hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/OrderingSuite.scala
@@ -4,6 +4,8 @@ import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.annotations._
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.ir.defs.{
   ApplyComparisonOp, ApplySpecial, ArraySort, ErrorIDs, GetField, I32, In, IsNA, Literal,
   MakeStream, NA, ToArray, ToDict, ToSet, ToStream, True,
@@ -14,9 +16,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.interfaces.SBaseStructValue
 import is.hail.types.virtual._
-import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import is.hail
 import org.apache.spark.sql.Row
@@ -453,7 +452,7 @@ class OrderingSuite extends HailSuite with ScalaCheckDrivenPropertyChecks {
     val compareGen =
       for {
         elt <- arbitrary[Type]
-        set: Set[Annotation] <- genNonMissingT(ctx, TSet(elt))
+        set <- genNonMissingT[Set[Annotation]](ctx, TSet(elt))
         v <- genNonMissing(ctx, elt)
       } yield (elt, set, v)
 
@@ -509,7 +508,7 @@ class OrderingSuite extends HailSuite with ScalaCheckDrivenPropertyChecks {
     val compareGen =
       for {
         tdict <- arbitrary[TDict]
-        dict: Map[Annotation, Annotation] <- genNonMissingT(ctx, tdict, innerRequired = false)
+        dict <- genNonMissingT[Map[Annotation, Annotation]](ctx, tdict, innerRequired = false)
         key <- genNonMissing(ctx, tdict.keyType, innerRequired = false)
       } yield (tdict, dict, key)
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala b/hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala
index becf2444242..7600438d7fe 100644
--- a/hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/PruneSuite.scala
@@ -2,6 +2,8 @@ package is.hail.expr.ir
 
 import is.hail.HailSuite
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.PruneDeadFields.TypeState
 import is.hail.expr.ir.defs._
@@ -10,8 +12,6 @@ import is.hail.methods.{ForceCountMatrixTable, ForceCountTable}
 import is.hail.rvd.RVD
 import is.hail.types._
 import is.hail.types.virtual._
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 
@@ -202,25 +202,25 @@ class PruneSuite extends HailSuite {
     false,
     false,
     new MatrixReader {
-      def pathsUsed: IndexedSeq[String] = FastSeq()
+      override def pathsUsed: IndexedSeq[String] = FastSeq()
 
       override def columnCount: Option[Int] = None
 
-      def partitionCounts: Option[IndexedSeq[Long]] = None
+      override def partitionCounts: Option[IndexedSeq[Long]] = None
 
-      def rowUIDType = TTuple(TInt64, TInt64)
-      def colUIDType = TTuple(TInt64, TInt64)
+      override def rowUIDType = TTuple(TInt64, TInt64)
+      override def colUIDType = TTuple(TInt64, TInt64)
 
-      def fullMatrixTypeWithoutUIDs: MatrixType = mat.typ
+      override def fullMatrixTypeWithoutUIDs: MatrixType = mat.typ
 
-      def lower(
+      override def lower(
         ctx: ExecuteContext,
         requestedType: MatrixType,
         dropCols: Boolean,
         dropRows: Boolean,
       ): TableIR = ???
 
-      def toJValue: JValue = ???
+      override def toJValue: JValue = ???
 
       override def renderShort(): String = "mr"
     },
diff --git a/hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala b/hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala
index e450fff53ce..8ba13a48e25 100644
--- a/hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/RandomSuite.scala
@@ -2,10 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.HailSuite
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.types.physical.stypes.concrete.{
   SCanonicalRNGStateSettable, SCanonicalRNGStateValue, SRNGState, SRNGStateStaticSizeValue,
 }
-import is.hail.utils.FastSeq
 
 import org.apache.commons.math3.distribution.ChiSquaredDistribution
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala b/hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala
index 4827b7801fc..596fa18a2db 100644
--- a/hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/RequirednessSuite.scala
@@ -1,6 +1,7 @@
 package is.hail.expr.ir
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.expr.Nat
 import is.hail.expr.ir.agg.CallStatsState
 import is.hail.expr.ir.defs._
@@ -13,7 +14,6 @@ import is.hail.types.physical.stypes.EmitType
 import is.hail.types.physical.stypes.interfaces.SStream
 import is.hail.types.physical.stypes.primitives.SInt32
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import scala.collection.mutable.ArrayBuffer
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala b/hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala
index 5341b6d58fd..75c4ed053e3 100644
--- a/hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/SimplifySuite.scala
@@ -2,10 +2,11 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs._
 import is.hail.types.virtual._
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.utils.Interval
 import is.hail.variant.Locus
 
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala
index d95cbf5cbf0..dd545371bff 100644
--- a/hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/StagedBTreeSuite.scala
@@ -3,6 +3,7 @@ package is.hail.expr.ir
 import is.hail.HailSuite
 import is.hail.annotations.Region
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.{valueToRichCodeInputBuffer, valueToRichCodeOutputBuffer}
 import is.hail.backend.ExecuteContext
 import is.hail.expr.ir.agg.{AppendOnlyBTree, BTreeKey}
 import is.hail.expr.ir.orderings.CodeOrdering
@@ -11,7 +12,6 @@ import is.hail.types.physical._
 import is.hail.types.physical.stypes.Int64SingleCodeType
 import is.hail.types.physical.stypes.interfaces.primitive
 import is.hail.types.physical.stypes.primitives.SInt64
-import is.hail.utils._
 
 import scala.collection.mutable
 
@@ -48,7 +48,7 @@ class TestBTreeKey(mb: EmitMethodBuilder[_]) extends BTreeKey {
   override def copy(cb: EmitCodeBuilder, src: Code[Long], dest: Code[Long]): Unit =
     cb += Region.copyFrom(src, dest, storageType.byteSize)
 
-  override def deepCopy(cb: EmitCodeBuilder, er: EmitRegion, src: Code[Long], dest: Code[Long])
+  override def deepCopy(cb: EmitCodeBuilder, r: Value[Region], src: Code[Long], dest: Code[Long])
     : Unit =
     copy(cb, src, dest)
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala
index 95f0e6b5cff..5ae18935e03 100644
--- a/hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/StagedMinHeapSuite.scala
@@ -4,6 +4,7 @@ import is.hail.HailSuite
 import is.hail.annotations.{Region, SafeIndexedSeq}
 import is.hail.asm4s._
 import is.hail.backend.ExecuteContext
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.functions.LocusFunctions
 import is.hail.expr.ir.streams.StagedMinHeap
 import is.hail.scalacheck._
@@ -11,7 +12,7 @@ import is.hail.types.physical.{PCanonicalArray, PCanonicalLocus, PInt32Required}
 import is.hail.types.physical.stypes.{SType, SValue}
 import is.hail.types.physical.stypes.concrete.SIndexablePointerValue
 import is.hail.types.physical.stypes.primitives.{SInt32, SInt32Value}
-import is.hail.utils.{using, FastSeq}
+import is.hail.utils.using
 import is.hail.variant.{Locus, ReferenceGenome}
 
 import org.scalacheck.Arbitrary.arbitrary
diff --git a/hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala
index 8be11a9b415..f6b72e140a7 100644
--- a/hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/StringFunctionsSuite.scala
@@ -2,10 +2,10 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs.{F32, I32, I64, MakeTuple, NA, Str}
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import org.json4s.jackson.JsonMethods
 import org.testng.annotations.{DataProvider, Test}
diff --git a/hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala b/hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala
index 15feff61df2..ea5882b3aa5 100644
--- a/hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/StringSliceSuite.scala
@@ -2,9 +2,9 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{I32, In, NA, Str}
 import is.hail.types.virtual.TString
-import is.hail.utils._
 
 import org.scalatest.Inspectors.forEvery
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala
index 3a7d13b1324..84d8feb071a 100644
--- a/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/TableIRSuite.scala
@@ -3,6 +3,8 @@ package is.hail.expr.ir
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
 import is.hail.annotations.SafeNDArray
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.Nat
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.analyses.PartitionCounts
diff --git a/hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala
index 629297bb6d8..bc51df922a6 100644
--- a/hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/TakeByAggregatorSuite.scala
@@ -3,11 +3,13 @@ package is.hail.expr.ir
 import is.hail.HailSuite
 import is.hail.annotations.{Region, SafeRow}
 import is.hail.asm4s._
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.collection.FastSeq
+import is.hail.collection.implicits._
 import is.hail.expr.ir.agg.TakeByRVAS
 import is.hail.types.VirtualTypeWithReq
 import is.hail.types.physical._
 import is.hail.types.physical.stypes.primitives.SInt32Value
-import is.hail.utils._
 
 import org.scalatest.Inspectors.forAll
 import org.scalatest.enablers.InspectorAsserting.assertingNatureOfAssertion
@@ -106,8 +108,7 @@ class TakeByAggregatorSuite extends HailSuite {
           new TakeByRVAS(VirtualTypeWithReq(PInt32Required), VirtualTypeWithReq(PInt32Required), kb)
         val ab = new agg.StagedArrayBuilder(PInt32Required, kb, argR)
         val rt = PCanonicalArray(tba.valueType)
-        val er = new EmitRegion(fb.apply_method, argR)
-        val rng = er.mb.newRNG(0)
+        val rng = fb.apply_method.threefryRandomEngine
 
         fb.emitWithBuilder { cb =>
           tba.createState(cb)
diff --git a/hail/hail/test/src/is/hail/expr/ir/TestUtils.scala b/hail/hail/test/src/is/hail/expr/ir/TestUtils.scala
index 58b8a23a773..1befdc772df 100644
--- a/hail/hail/test/src/is/hail/expr/ir/TestUtils.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/TestUtils.scala
@@ -1,11 +1,11 @@
 package is.hail.expr.ir
 
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{
   ApplyAggOp, ApplyScanOp, F64, I32, Literal, MakeArray, MakeStream, MakeStruct, MakeTuple, NA, Ref,
   TableAggregate, TableCollect, ToDict, ToSet, ToStream,
 }
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 import is.hail.variant.Call
 
 object TestUtils {
diff --git a/hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala b/hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala
index 83d165a846f..5268a5afd54 100644
--- a/hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/TrapNodeSuite.scala
@@ -2,9 +2,9 @@ package is.hail.expr.ir
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{ArrayRef, Die, GetTupleElement, I32, If, IsNA, Literal, Str, Trap}
 import is.hail.types.virtual._
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala b/hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala
index 4b258e8ff09..dc8e260806c 100644
--- a/hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/agg/DownsampleSuite.scala
@@ -22,7 +22,7 @@ class DownsampleSuite extends HailSuite {
 
     val stagedPool = fb.newLocal[RegionPool]("pool")
 
-    val rng = fb.newRNG(0)
+    val rng = fb.threefryRandomEngine
     val i = fb.newLocal[Int]()
 
     val x = fb.newLocal[Double]()
diff --git a/hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala b/hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala
index 67db8f6a79b..25b6ca18bfa 100644
--- a/hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/agg/StagedBlockLinkedListSuite.scala
@@ -3,11 +3,11 @@ package is.hail.expr.ir.agg
 import is.hail.HailSuite
 import is.hail.annotations.{Region, SafeRow, ScalaToRegionValue}
 import is.hail.asm4s.Code
+import is.hail.asm4s.implicits.valueToRichCodeRegion
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.compat.mutable.GrowableCompat
 import is.hail.expr.ir.{EmitCode, EmitFunctionBuilder}
 import is.hail.types.physical._
-import is.hail.utils._
-import is.hail.utils.compat.immutable.ArraySeq
-import is.hail.utils.compat.mutable.GrowableCompat
 
 import org.testng.Assert._
 import org.testng.annotations.Test
@@ -127,8 +127,8 @@ class StagedBlockLinkedListSuite extends HailSuite {
 
     private var ptr = 0L
 
-    def clear(): Unit = ptr = initF(region)
-    def addOne(e: E): this.type = { pushF(region, ptr, e); this }
+    override def clear(): Unit = ptr = initF(region)
+    override def addOne(e: E): this.type = { pushF(region, ptr, e); this }
     def ++=(other: BlockLinkedList[E]): this.type = { appendF(region, ptr, other); this }
     def toIndexedSeq: IndexedSeq[E] = materializeF(region, ptr)
 
diff --git a/hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala b/hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala
index 9b88be8b9cc..4431388db35 100644
--- a/hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/analyses/SemanticHashSuite.scala
@@ -1,13 +1,13 @@
 package is.hail.expr.ir.analyses
 
-import is.hail.{HAIL_PRETTY_VERSION, HailSuite}
+import is.hail.{HailSuite, PrettyVersion}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.defs._
 import is.hail.io.fs.{FS, FakeFS, FakeURL, FileListEntry}
 import is.hail.linalg.BlockMatrixMetadata
 import is.hail.rvd.AbstractRVDSpec
 import is.hail.types.virtual._
-import is.hail.utils.FastSeq
 
 import java.io.FileNotFoundException
 import java.lang
@@ -365,7 +365,7 @@ class SemanticHashSuite extends HailSuite {
           override def file_version: Int =
             1
           override def hail_version: String =
-            HAIL_PRETTY_VERSION
+            PrettyVersion
           override def components: Map[String, ComponentSpec] =
             Map.empty
           override def toJValue: JValue = ???
diff --git a/hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala b/hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
index 4ef8a0b7adb..81ca537f439 100644
--- a/hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/lowering/LowerDistributedSortSuite.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.lowering
 
 import is.hail.{ExecStrategy, HailSuite, TestUtils}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{
   mapIR, Ascending, Descending, LoweringAnalyses, SortField, TableIR, TableMapRows, TableRange,
 }
@@ -12,7 +13,6 @@ import is.hail.expr.ir.defs.{
 import is.hail.expr.ir.lowering.LowerDistributedSort.samplePartition
 import is.hail.types.RTable
 import is.hail.types.virtual.{TArray, TInt32, TStruct}
-import is.hail.utils.FastSeq
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala b/hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala
index be46154ad92..3294c639139 100644
--- a/hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala
+++ b/hail/hail/test/src/is/hail/expr/ir/table/TableGenSuite.scala
@@ -2,6 +2,7 @@ package is.hail.expr.ir.table
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir._
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.defs.{
@@ -11,7 +12,7 @@ import is.hail.expr.ir.defs.{
 import is.hail.expr.ir.lowering.{DArrayLowering, LowerTableIR}
 import is.hail.rvd.RVDPartitioner
 import is.hail.types.virtual._
-import is.hail.utils.{FastSeq, HailException, Interval}
+import is.hail.utils.{HailException, Interval}
 
 import org.apache.spark.SparkException
 import org.apache.spark.sql.Row
diff --git a/hail/hail/test/src/is/hail/utils/RichArraySuite.scala b/hail/hail/test/src/is/hail/io/ArrayImpexSuite.scala
similarity index 50%
rename from hail/hail/test/src/is/hail/utils/RichArraySuite.scala
rename to hail/hail/test/src/is/hail/io/ArrayImpexSuite.scala
index b7793450052..96d7b13b25f 100644
--- a/hail/hail/test/src/is/hail/utils/RichArraySuite.scala
+++ b/hail/hail/test/src/is/hail/io/ArrayImpexSuite.scala
@@ -1,22 +1,21 @@
-package is.hail.utils
+package is.hail.io
 
 import is.hail.HailSuite
-import is.hail.utils.richUtils.RichArray
 
 import org.testng.annotations.Test
 
-class RichArraySuite extends HailSuite {
+class ArrayImpexSuite extends HailSuite {
   @Test def testArrayImpex(): Unit = {
     val file = ctx.createTmpPath("test")
     val a = Array.fill[Double](100)(util.Random.nextDouble())
     val a2 = new Array[Double](100)
 
-    RichArray.exportToDoubles(fs, file, a, bufSize = 32)
-    RichArray.importFromDoubles(fs, file, a2, bufSize = 16)
+    ArrayImpex.exportToDoubles(fs, file, a, bufSize = 32)
+    ArrayImpex.importFromDoubles(fs, file, a2, bufSize = 16)
     assert(a === a2)
 
     interceptFatal("Premature") {
-      RichArray.importFromDoubles(fs, file, new Array[Double](101), bufSize = 64)
+      ArrayImpex.importFromDoubles(fs, file, new Array[Double](101), bufSize = 64)
     }
   }
 }
diff --git a/hail/hail/test/src/is/hail/io/AvroReaderSuite.scala b/hail/hail/test/src/is/hail/io/AvroReaderSuite.scala
index af41fdeb81a..54efc08316a 100644
--- a/hail/hail/test/src/is/hail/io/AvroReaderSuite.scala
+++ b/hail/hail/test/src/is/hail/io/AvroReaderSuite.scala
@@ -2,9 +2,10 @@ package is.hail.io
 
 import is.hail.{ExecStrategy, HailSuite}
 import is.hail.ExecStrategy.ExecStrategy
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.defs.{I64, MakeStruct, ReadPartition, Str, ToArray}
 import is.hail.io.avro.AvroPartitionReader
-import is.hail.utils.{fatal, using, FastSeq}
+import is.hail.utils.{fatal, using}
 
 import org.apache.avro.SchemaBuilder
 import org.apache.avro.file.DataFileWriter
diff --git a/hail/hail/test/src/is/hail/io/IndexSuite.scala b/hail/hail/test/src/is/hail/io/IndexSuite.scala
index 7b62b088ffb..1e094021096 100644
--- a/hail/hail/test/src/is/hail/io/IndexSuite.scala
+++ b/hail/hail/test/src/is/hail/io/IndexSuite.scala
@@ -2,6 +2,7 @@ package is.hail.io
 
 import is.hail.HailSuite
 import is.hail.annotations.Annotation
+import is.hail.collection.implicits.{toRichIterable, toRichIterator}
 import is.hail.io.index._
 import is.hail.types.physical.{PCanonicalString, PCanonicalStruct, PInt32, PType}
 import is.hail.types.virtual._
diff --git a/hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala b/hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala
index 0c30b9813df..c1a1315ee13 100644
--- a/hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala
+++ b/hail/hail/test/src/is/hail/io/compress/BGzipCodecSuite.scala
@@ -1,8 +1,10 @@
 package is.hail.io.compress
 
 import is.hail.HailSuite
+import is.hail.collection.implicits.toRichIterator
 import is.hail.expr.ir.GenericLines
 import is.hail.scalacheck.ApplicativeGenOps
+import is.hail.sparkextras.implicits._
 import is.hail.utils._
 
 import scala.collection.mutable
@@ -241,8 +243,8 @@ class BGzipCodecSuite extends HailSuite with ScalaCheckDrivenPropertyChecks {
           assert(decompIS.getVirtualOffset() == vOff);
           uncompIS.seek(uOff.toLong + extra)
 
-          val decompRead = decompIS.readRepeatedly(decompData)
-          val uncompRead = uncompIS.readRepeatedly(uncompData)
+          val decompRead = decompIS.readNBytes(decompData, 0, decompData.length)
+          val uncompRead = uncompIS.readNBytes(uncompData, 0, uncompData.length)
 
           assert(
             decompRead == uncompRead,
diff --git a/hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala b/hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala
index 265c17a9d00..b0a0ffa3679 100644
--- a/hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala
+++ b/hail/hail/test/src/is/hail/linalg/BlockMatrixSuite.scala
@@ -1,10 +1,12 @@
 package is.hail.linalg
 
 import is.hail.HailSuite
+import is.hail.collection.implicits.toRichIterable
 import is.hail.expr.ir.{CompileAndEvaluate, TableLiteral}
 import is.hail.expr.ir.defs.{GetField, TableCollect}
 import is.hail.expr.ir.lowering.LoweringPipeline
 import is.hail.linalg.BlockMatrix.ops._
+import is.hail.linalg.implicits._
 import is.hail.scalacheck._
 import is.hail.types.virtual.{TFloat64, TInt64, TStruct}
 import is.hail.utils._
diff --git a/hail/hail/test/src/is/hail/linalg/MatrixSparsitySuite.scala b/hail/hail/test/src/is/hail/linalg/MatrixSparsitySuite.scala
index 2448d32e4a5..09b1321b537 100644
--- a/hail/hail/test/src/is/hail/linalg/MatrixSparsitySuite.scala
+++ b/hail/hail/test/src/is/hail/linalg/MatrixSparsitySuite.scala
@@ -1,6 +1,6 @@
 package is.hail.linalg
 
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.collection.compat.immutable.ArraySeq
 
 import org.scalatestplus.testng.TestNGSuite
 import org.testng.annotations.{DataProvider, Test}
diff --git a/hail/hail/test/src/is/hail/utils/RichDenseMatrixDoubleSuite.scala b/hail/hail/test/src/is/hail/linalg/RichDenseMatrixDoubleSuite.scala
similarity index 91%
rename from hail/hail/test/src/is/hail/utils/RichDenseMatrixDoubleSuite.scala
rename to hail/hail/test/src/is/hail/linalg/RichDenseMatrixDoubleSuite.scala
index 380d03046e1..b8758b1219b 100644
--- a/hail/hail/test/src/is/hail/utils/RichDenseMatrixDoubleSuite.scala
+++ b/hail/hail/test/src/is/hail/linalg/RichDenseMatrixDoubleSuite.scala
@@ -1,8 +1,7 @@
-package is.hail.utils
+package is.hail.linalg
 
 import is.hail.HailSuite
-import is.hail.linalg.BlockMatrix
-import is.hail.utils.richUtils.RichDenseMatrixDouble
+import is.hail.linalg.implicits._
 
 import breeze.linalg.{DenseMatrix => BDM}
 import org.testng.annotations.Test
diff --git a/hail/hail/test/src/is/hail/utils/RichIndexedRowMatrixSuite.scala b/hail/hail/test/src/is/hail/linalg/RichIndexedRowMatrixSuite.scala
similarity index 97%
rename from hail/hail/test/src/is/hail/utils/RichIndexedRowMatrixSuite.scala
rename to hail/hail/test/src/is/hail/linalg/RichIndexedRowMatrixSuite.scala
index dba42bffa78..b0250b8d5fe 100644
--- a/hail/hail/test/src/is/hail/utils/RichIndexedRowMatrixSuite.scala
+++ b/hail/hail/test/src/is/hail/linalg/RichIndexedRowMatrixSuite.scala
@@ -1,7 +1,8 @@
-package is.hail.utils
+package is.hail.linalg
 
 import is.hail.HailSuite
 import is.hail.linalg.BlockMatrix.ops._
+import is.hail.linalg.implicits.toRichIndexedRowMatrix
 
 import breeze.linalg.{DenseMatrix => BDM}
 import org.apache.spark.mllib.linalg.Vectors
diff --git a/hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala b/hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala
index 157f6cd746f..5da62b3110f 100644
--- a/hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala
+++ b/hail/hail/test/src/is/hail/linalg/RowMatrixSuite.scala
@@ -1,8 +1,8 @@
 package is.hail.linalg
 
 import is.hail.HailSuite
+import is.hail.expr.ir.ExportType
 import is.hail.scalacheck._
-import is.hail.utils._
 
 import breeze.linalg.DenseMatrix
 import org.scalatest
diff --git a/hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala b/hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala
index 2602564ae97..29101e49ce9 100644
--- a/hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala
+++ b/hail/hail/test/src/is/hail/methods/LocalLDPruneSuite.scala
@@ -3,6 +3,7 @@ package is.hail.methods
 import is.hail.HailSuite
 import is.hail.annotations.Annotation
 import is.hail.expr.ir.{Interpret, MatrixValue, TableValue}
+import is.hail.sparkextras.implicits.toRichRDD
 import is.hail.utils._
 import is.hail.variant._
 
diff --git a/hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala b/hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala
index 4e6713c76be..c43270b2baa 100644
--- a/hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala
+++ b/hail/hail/test/src/is/hail/rvd/RVDPartitionerSuite.scala
@@ -1,8 +1,9 @@
 package is.hail.rvd
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.types.virtual.{TInt32, TStruct}
-import is.hail.utils.{FastSeq, Interval}
+import is.hail.utils.Interval
 
 import org.apache.spark.sql.Row
 import org.testng.ITestContext
diff --git a/hail/hail/test/src/is/hail/scalacheck/ArbitraryGenomicInstances.scala b/hail/hail/test/src/is/hail/scalacheck/ArbitraryGenomicInstances.scala
index 05b673a824f..b0b6df14076 100644
--- a/hail/hail/test/src/is/hail/scalacheck/ArbitraryGenomicInstances.scala
+++ b/hail/hail/test/src/is/hail/scalacheck/ArbitraryGenomicInstances.scala
@@ -1,7 +1,8 @@
 package is.hail.scalacheck
 
 import is.hail.annotations.Annotation
-import is.hail.utils.{toRichIterable, triangle, uniqueMaxIndex}
+import is.hail.collection.implicits.toRichIterable
+import is.hail.utils.{triangle, uniqueMaxIndex}
 import is.hail.variant._
 import is.hail.variant.Genotype.gqFromPL
 import is.hail.variant.Sex.Sex
diff --git a/hail/hail/test/src/is/hail/services/BatchClientSuite.scala b/hail/hail/test/src/is/hail/services/BatchClientSuite.scala
index 7c340611378..fcc91e23151 100644
--- a/hail/hail/test/src/is/hail/services/BatchClientSuite.scala
+++ b/hail/hail/test/src/is/hail/services/BatchClientSuite.scala
@@ -1,7 +1,8 @@
 package is.hail.services
 
-import is.hail.{services, HAIL_REVISION}
+import is.hail.{services, Revision}
 import is.hail.backend.service.Main
+import is.hail.collection.FastSeq
 import is.hail.services.JobGroupStates.Failure
 import is.hail.services.oauth2.CloudCredentials
 import is.hail.utils._
@@ -165,7 +166,7 @@ class BatchClientSuite extends TestNGSuite {
             always_run = false,
             process = JvmJob(
               command = Array(Main.TEST),
-              spec = GitRevision(HAIL_REVISION),
+              spec = GitRevision(Revision),
               profile = false,
             ),
           )
diff --git a/hail/hail/test/src/is/hail/utils/RichRDDSuite.scala b/hail/hail/test/src/is/hail/sparkextras/RichRDDSuite.scala
similarity index 94%
rename from hail/hail/test/src/is/hail/utils/RichRDDSuite.scala
rename to hail/hail/test/src/is/hail/sparkextras/RichRDDSuite.scala
index bf793008c15..d9321aff26e 100644
--- a/hail/hail/test/src/is/hail/utils/RichRDDSuite.scala
+++ b/hail/hail/test/src/is/hail/sparkextras/RichRDDSuite.scala
@@ -1,6 +1,8 @@
-package is.hail.utils
+package is.hail.sparkextras
 
 import is.hail.HailSuite
+import is.hail.expr.ir.ExportType
+import is.hail.sparkextras.implicits._
 
 import org.testng.annotations.Test
 
diff --git a/hail/hail/test/src/is/hail/stats/eigSymDSuite.scala b/hail/hail/test/src/is/hail/stats/eigSymDSuite.scala
index 5db343659b0..2d12073f217 100644
--- a/hail/hail/test/src/is/hail/stats/eigSymDSuite.scala
+++ b/hail/hail/test/src/is/hail/stats/eigSymDSuite.scala
@@ -1,6 +1,7 @@
 package is.hail.stats
 
 import is.hail.HailSuite
+import is.hail.linalg.implicits._
 import is.hail.utils._
 
 import breeze.linalg.{eigSym, svd, DenseMatrix, DenseVector}
diff --git a/hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala b/hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala
index 1db29ca9efa..4bf3dbbc575 100644
--- a/hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala
+++ b/hail/hail/test/src/is/hail/types/encoded/ETypeSuite.scala
@@ -3,11 +3,11 @@ package is.hail.types.encoded
 import is.hail.HailSuite
 import is.hail.annotations.{Annotation, Region, SafeNDArray, SafeRow}
 import is.hail.asm4s.Code
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitFunctionBuilder
 import is.hail.io._
 import is.hail.rvd.AbstractRVDSpec
 import is.hail.types.physical._
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 import org.json4s.jackson.Serialization
diff --git a/hail/hail/test/src/is/hail/types/physical/PContainerTest.scala b/hail/hail/test/src/is/hail/types/physical/PContainerTest.scala
index b1fd8482472..db8d180a048 100644
--- a/hail/hail/test/src/is/hail/types/physical/PContainerTest.scala
+++ b/hail/hail/test/src/is/hail/types/physical/PContainerTest.scala
@@ -2,8 +2,8 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Annotation, Region, ScalaToRegionValue}
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.EmitFunctionBuilder
-import is.hail.utils._
 
 import org.scalatest.Inspectors.forAll
 import org.scalatest.enablers.InspectorAsserting.assertingNatureOfAssertion
diff --git a/hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala b/hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala
index 61a02d4a22c..93c81e40472 100644
--- a/hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala
+++ b/hail/hail/test/src/is/hail/types/physical/PNDArraySuite.scala
@@ -2,10 +2,10 @@ package is.hail.types.physical
 
 import is.hail.annotations.{Region, SafeNDArray, UnsafeRow}
 import is.hail.asm4s._
+import is.hail.collection.FastSeq
 import is.hail.expr.ir.{EmitCodeBuilder, EmitFunctionBuilder}
 import is.hail.methods.LocalWhitening
 import is.hail.types.physical.stypes.interfaces.{ColonIndex => Colon, _}
-import is.hail.utils._
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.Test
@@ -55,7 +55,11 @@ class PNDArraySuite extends PhysicalTestUtils {
         val T = vecType.constructUninitialized(FastSeq(btwpn), cb, region)
 
         A.coiterateMutate(cb, region) { case Seq(_) =>
-          primitive(cb.memoize(cb.emb.newRNG(0L).invoke[Double]("rnorm")))
+          primitive(cb.memoize(cb.emb.threefryRandomEngine.invoke[Double, Double, Double](
+            "rnorm",
+            0,
+            1,
+          )))
         }
         Acopy.coiterateMutate(cb, region, (A, "A")) { case Seq(_, a) => a }
 
@@ -118,7 +122,11 @@ class PNDArraySuite extends PhysicalTestUtils {
         val T = vecType.constructUninitialized(FastSeq(btn), FastSeq(8), cb, region)
 
         A.coiterateMutate(cb, region) { case Seq(_) =>
-          primitive(cb.memoize(cb.emb.newRNG(0L).invoke[Double]("rnorm")))
+          primitive(cb.memoize(cb.emb.threefryRandomEngine.invoke[Double, Double, Double](
+            "rnorm",
+            0,
+            1,
+          )))
         }
         Acopy.coiterateMutate(cb, region, (A, "A")) { case Seq(_, a) => a }
         SNDArray.geqrt_full(cb, Acopy, Q, R, T, work, blocksize)
@@ -235,7 +243,11 @@ class PNDArraySuite extends PhysicalTestUtils {
         val state = new LocalWhitening(cb, m, w, n, blocksize, region, false)
 
         Aorig.coiterateMutate(cb, region) { case Seq(_) =>
-          primitive(cb.memoize(cb.emb.newRNG(0L).invoke[Double]("rnorm")))
+          primitive(cb.memoize(cb.emb.threefryRandomEngine.invoke[Double, Double, Double](
+            "rnorm",
+            0,
+            1,
+          )))
         }
         A.coiterateMutate(cb, region, (Aorig.slice(cb, Colon, (w, null)), "Aorig")) {
           case Seq(_, a) => a
@@ -323,7 +335,11 @@ class PNDArraySuite extends PhysicalTestUtils {
         val A = matType.constructUninitialized(FastSeq(m, n), cb, region)
 
         Aorig.coiterateMutate(cb, region) { case Seq(_) =>
-          primitive(cb.memoize(cb.emb.newRNG(0L).invoke[Double]("rnorm")))
+          primitive(cb.memoize(cb.emb.threefryRandomEngine.invoke[Double, Double, Double](
+            "rnorm",
+            0,
+            1,
+          )))
         }
         SNDArray.copyMatrix(cb, " ", Aorig, A)
 
diff --git a/hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala b/hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala
index 2270704255a..f04dbdbe337 100644
--- a/hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala
+++ b/hail/hail/test/src/is/hail/types/physical/PTypeSuite.scala
@@ -1,6 +1,7 @@
 package is.hail.types.physical
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.rvd.AbstractRVDSpec
 import is.hail.types.virtual._
 import is.hail.utils._
diff --git a/hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala b/hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
index 7632c9958ce..0e6db0d34f1 100644
--- a/hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
+++ b/hail/hail/test/src/is/hail/types/physical/stypes/concrete/SStructViewSuite.scala
@@ -1,11 +1,11 @@
 package is.hail.types.physical.stypes.concrete
 
 import is.hail.HailSuite
+import is.hail.collection.FastSeq
 import is.hail.types.physical.stypes.SType
 import is.hail.types.physical.stypes.interfaces.SBaseStruct
 import is.hail.types.tcoerce
 import is.hail.types.virtual.{TInt32, TInt64, TStruct}
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.Test
 
diff --git a/hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala b/hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala
index 77f59bb686c..e2391d2b152 100644
--- a/hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala
+++ b/hail/hail/test/src/is/hail/types/virtual/TStructSuite.scala
@@ -2,7 +2,7 @@ package is.hail.types.virtual
 
 import is.hail.HailSuite
 import is.hail.annotations.{Annotation, Inserter}
-import is.hail.utils.FastSeq
+import is.hail.collection.FastSeq
 
 import org.apache.spark.sql.Row
 import org.testng.annotations.{DataProvider, Test}
diff --git a/hail/hail/test/src/is/hail/utils/IntervalSuite.scala b/hail/hail/test/src/is/hail/utils/IntervalSuite.scala
index 6128ed7a412..1c66eaad377 100644
--- a/hail/hail/test/src/is/hail/utils/IntervalSuite.scala
+++ b/hail/hail/test/src/is/hail/utils/IntervalSuite.scala
@@ -3,9 +3,10 @@ package is.hail.utils
 import is.hail.HailSuite
 import is.hail.annotations.ExtendedOrdering
 import is.hail.backend.{ExecuteContext, HailStateManager}
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.collection.implicits.toRichIterable
 import is.hail.rvd.RVDPartitioner
 import is.hail.types.virtual.{TInt32, TStruct}
-import is.hail.utils.compat.immutable.ArraySeq
 
 import org.apache.spark.sql.Row
 import org.scalatest.Inspectors.forAll
diff --git a/hail/hail/src/is/hail/utils/MultiArray2.scala b/hail/hail/test/src/is/hail/utils/MultiArray2.scala
similarity index 89%
rename from hail/hail/src/is/hail/utils/MultiArray2.scala
rename to hail/hail/test/src/is/hail/utils/MultiArray2.scala
index c72c9114071..ea04dc92a58 100644
--- a/hail/hail/src/is/hail/utils/MultiArray2.scala
+++ b/hail/hail/test/src/is/hail/utils/MultiArray2.scala
@@ -1,10 +1,7 @@
 package is.hail.utils
 
-import scala.collection.immutable.IndexedSeq
 import scala.reflect.ClassTag
 
-import java.io.Serializable
-
 class MultiArray2[@specialized(Int, Long, Float, Double, Boolean) T](
   val n1: Int,
   val n2: Int,
@@ -17,23 +14,23 @@ class MultiArray2[@specialized(Int, Long, Float, Double, Boolean) T](
   class Row(val i: Int) extends IndexedSeq[T] {
     require(i >= 0 && i < n1)
 
-    def apply(j: Int): T = {
+    override def apply(j: Int): T = {
       if (j < 0 || j >= length) throw new ArrayIndexOutOfBoundsException
       a(i * n2 + j)
     }
 
-    def length: Int = n2
+    override def length: Int = n2
   }
 
   class Column(val j: Int) extends IndexedSeq[T] {
     require(j >= 0 && j < n2)
 
-    def apply(i: Int): T = {
+    override def apply(i: Int): T = {
       if (i < 0 || i >= length) throw new ArrayIndexOutOfBoundsException
       a(i * n2 + j)
     }
 
-    def length: Int = n1
+    override def length: Int = n1
   }
 
   def row(i: Int) = new Row(i)
@@ -73,7 +70,7 @@ class MultiArray2[@specialized(Int, Long, Float, Double, Boolean) T](
     new MultiArray2(n1, n2, a.zip(other.a))
   }
 
-  def iterator: Iterator[T] = a.iterator
+  override def iterator: Iterator[T] = a.iterator
 }
 
 object MultiArray2 {
diff --git a/hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala b/hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala
index 31145ee013d..7bdc450fb8c 100644
--- a/hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala
+++ b/hail/hail/test/src/is/hail/utils/RowIntervalSuite.scala
@@ -1,6 +1,7 @@
 package is.hail.utils
 
 import is.hail.{ExecStrategy, HailSuite}
+import is.hail.collection.FastSeq
 import is.hail.expr.ir
 import is.hail.expr.ir.defs.In
 import is.hail.rvd.{PartitionBoundOrdering, RVDPartitioner}
diff --git a/hail/hail/test/src/is/hail/utils/UtilsSuite.scala b/hail/hail/test/src/is/hail/utils/UtilsSuite.scala
index f0466dc1fb7..66d3c1aa787 100644
--- a/hail/hail/test/src/is/hail/utils/UtilsSuite.scala
+++ b/hail/hail/test/src/is/hail/utils/UtilsSuite.scala
@@ -1,7 +1,9 @@
 package is.hail.utils
 
 import is.hail.HailSuite
+import is.hail.collection.implicits.{toRichIterable, toRichOrderedArray, toRichOrderedSeq}
 import is.hail.io.fs.HadoopFS
+import is.hail.sparkextras.implicits._
 
 import org.apache.spark.storage.StorageLevel
 import org.scalacheck.Gen
@@ -84,9 +86,11 @@ class UtilsSuite extends HailSuite with ScalaCheckDrivenPropertyChecks {
     val fs = new HadoopFS(new SerializableHadoopConfiguration(sc.hadoopConfiguration))
 
     val partFileNames = fs.glob(getTestResource("part-*"))
-      .sortBy(fileListEntry => getPartNumber(fileListEntry.getPath)).map(_.getPath.split(
-        "/"
-      ).last)
+      .sortBy(fileListEntry => is.hail.io.fs.getPartNumber(fileListEntry.getPath)).map(
+        _.getPath.split(
+          "/"
+        ).last
+      )
 
     assert(partFileNames(0) == "part-40001" && partFileNames(1) == "part-100001")
   }
diff --git a/hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala b/hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
index 4a83ef9a6e0..8f0e4a1089c 100644
--- a/hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
+++ b/hail/hail/test/src/is/hail/utils/prettyPrint/PrettyPrintWriterSuite.scala
@@ -1,6 +1,6 @@
 package is.hail.utils.prettyPrint
 
-import is.hail.utils.toRichIterator
+import is.hail.collection.implicits.toRichIterator
 
 import scala.jdk.CollectionConverters._
 
diff --git a/hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala b/hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala
index 70486a059c4..5de4fe23683 100644
--- a/hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala
+++ b/hail/hail/test/src/is/hail/variant/vsm/PartitioningSuite.scala
@@ -2,11 +2,11 @@ package is.hail.variant.vsm
 
 import is.hail.HailSuite
 import is.hail.annotations.BroadcastRow
+import is.hail.collection.FastSeq
 import is.hail.expr.ir
 import is.hail.expr.ir.{Interpret, MatrixAnnotateRowsTable, TableLiteral, TableValue}
 import is.hail.rvd.RVD
 import is.hail.types.virtual.{TInt32, TStruct, TableType}
-import is.hail.utils.FastSeq
 
 import org.testng.annotations.Test
 
diff --git a/hail/hail/utils/package.mill b/hail/hail/utils/package.mill
new file mode 100644
index 00000000000..a51e16afdac
--- /dev/null
+++ b/hail/hail/utils/package.mill
@@ -0,0 +1,36 @@
+package build.hail.utils
+
+import mill.T
+import mill.api.Cross
+import mill.scalalib.{CrossScalaModule, Dep}
+
+import build.Settings
+import build.HailScalaModule
+
+import millbuild.BuildConfig.*
+import millbuild.MvnCoordinate.*
+
+object `package` extends Cross[HailUtils](enabledScalaVersions)
+trait HailUtils extends HailScalaModule, CrossScalaModule:
+  override def crossScalaVersion: String =
+    Settings.scalaMinorVersions(crossValue)
+
+  override def bomMvnDeps: T[Seq[Dep]] =
+    Seq(
+      `log4j-bom` :: "2.22.0",
+    )
+
+  override def compileMvnDeps: T[Seq[Dep]] =
+    Vector[Dep](
+      `json4s-jackson` :: "3.7.0-M11",
+      `log4j-core`,
+      `zstd-jni` :: "1.5.5-4",
+      `scalac-compat-annotation` :: "0.1.4",
+    )
+
+  override def mvnDeps: T[Seq[Dep]] =
+    Vector[Dep](
+      (`log4j-api-scala` :: "13.1.0").excludeOrg("*"),
+      `scala-collection-compat`,
+      `sourcecode` :: "0.4.2",
+    )
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/immutable/ArraySeq.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/ArraySeq.scala
similarity index 96%
rename from hail/hail/src-2.12/is/hail/utils/compat/immutable/ArraySeq.scala
rename to hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/ArraySeq.scala
index 4cf63e1ca0d..e52a6136946 100644
--- a/hail/hail/src-2.12/is/hail/utils/compat/immutable/ArraySeq.scala
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/ArraySeq.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.compat.immutable
+package is.hail.collection.compat.immutable
 
 import scala.collection.compat.IterableOnce
 import scala.collection.generic.CanBuildFrom
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/immutable/package.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/package.scala
similarity index 79%
rename from hail/hail/src-2.12/is/hail/utils/compat/immutable/package.scala
rename to hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/package.scala
index 2faa2784550..e4504319f0b 100644
--- a/hail/hail/src-2.12/is/hail/utils/compat/immutable/package.scala
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/immutable/package.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.compat
+package is.hail.collection.compat
 
 package object immutable {
   // scalafix:off ForbiddenSymbol
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/GrowableCompat.scala
similarity index 80%
rename from hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala
rename to hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/GrowableCompat.scala
index 44709a9df34..1cc851853ea 100644
--- a/hail/hail/src-2.12/is/hail/utils/compat/mutable/GrowableCompat.scala
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/GrowableCompat.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.compat.mutable
+package is.hail.collection.compat.mutable
 
 trait GrowableCompat[-A] extends Growable[A] {
   override def +=(elem: A): this.type = addOne(elem)
diff --git a/hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/ShrinkableCompat.scala
similarity index 79%
rename from hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala
rename to hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/ShrinkableCompat.scala
index c6f90b162ea..b6a9b3f208a 100644
--- a/hail/hail/src-2.12/is/hail/utils/compat/mutable/ShrinkableCompat.scala
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/ShrinkableCompat.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.compat.mutable
+package is.hail.collection.compat.mutable
 
 trait ShrinkableCompat[-A] extends Shrinkable[A] {
   override def -=(elem: A): this.type = subtractOne(elem)
diff --git a/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/package.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/package.scala
new file mode 100644
index 00000000000..e85c36fdcd9
--- /dev/null
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/mutable/package.scala
@@ -0,0 +1,10 @@
+package is.hail.collection.compat
+
+package object mutable {
+  // scalafix:off ForbiddenSymbol
+  type AnyRefMap[K <: AnyRef, V] = scala.collection.mutable.AnyRefMap[K, V]
+  val AnyRefMap = scala.collection.mutable.AnyRefMap
+
+  type Growable[-A] = scala.collection.generic.Growable[A]
+  type Shrinkable[-A] = scala.collection.generic.Shrinkable[A]
+}
diff --git a/hail/hail/utils/src-2.12/is/hail/collection/compat/package.scala b/hail/hail/utils/src-2.12/is/hail/collection/compat/package.scala
new file mode 100644
index 00000000000..ccfca98d703
--- /dev/null
+++ b/hail/hail/utils/src-2.12/is/hail/collection/compat/package.scala
@@ -0,0 +1,26 @@
+package is.hail.collection
+
+import is.hail.collection.compat.immutable.ArraySeq
+
+import scala.collection.compat.Factory
+import scala.collection.mutable.WrappedArray
+import scala.reflect.ClassTag
+
+package compat {
+  class ArrayOps[A](val a: WrappedArray[A]) extends AnyVal {
+    def sortInPlace()(implicit at: ClassTag[A], ord: Ordering[A]): WrappedArray[A] = {
+      scala.util.Sorting.stableSort(a.array)
+      a
+    }
+
+    def sortInPlaceBy[B](f: A => B)(implicit at: ClassTag[A], ord: Ordering[B]): WrappedArray[A] =
+      sortInPlace()(at, ord = ord on f)
+  }
+}
+
+package object compat {
+  implicit def arraySeqbf[A: ClassTag](ob: ArraySeq.type): Factory[A, ArraySeq[A]] =
+    ob.canBuildFrom[A]
+
+  implicit def toArrayOps[A: ClassTag](a: Array[A]): ArrayOps[A] = new ArrayOps(a)
+}
diff --git a/hail/hail/src-2.12/scala/collection/parallel/CollectionConverters.scala b/hail/hail/utils/src-2.12/scala/collection/parallel/CollectionConverters.scala
similarity index 100%
rename from hail/hail/src-2.12/scala/collection/parallel/CollectionConverters.scala
rename to hail/hail/utils/src-2.12/scala/collection/parallel/CollectionConverters.scala
diff --git a/hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala b/hail/hail/utils/src-2.13/is/hail/collection/compat/immutable/package.scala
similarity index 80%
rename from hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala
rename to hail/hail/utils/src-2.13/is/hail/collection/compat/immutable/package.scala
index 0e576162a2a..0e60c50ba38 100644
--- a/hail/hail/src-2.13/is/hail/utils/compat/immutable/package.scala
+++ b/hail/hail/utils/src-2.13/is/hail/collection/compat/immutable/package.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.compat
+package is.hail.collection.compat
 
 package object immutable {
   type ArraySeq[+A] = scala.collection.immutable.ArraySeq[A]
diff --git a/hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala b/hail/hail/utils/src-2.13/is/hail/collection/compat/mutable/package.scala
similarity index 60%
rename from hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala
rename to hail/hail/utils/src-2.13/is/hail/collection/compat/mutable/package.scala
index 1918e4e5942..e25208b89df 100644
--- a/hail/hail/src-2.13/is/hail/utils/compat/mutable/package.scala
+++ b/hail/hail/utils/src-2.13/is/hail/collection/compat/mutable/package.scala
@@ -1,6 +1,9 @@
-package is.hail.utils.compat
+package is.hail.collection.compat
 
 package object mutable {
+  type AnyRefMap[K, V] = scala.collection.mutable.HashMap[K, V]
+  val AnyRefMap = scala.collection.mutable.HashMap
+
   type Growable[-A] = scala.collection.mutable.Growable[A]
   type GrowableCompat[-A] = Growable[A]
   type Shrinkable[-A] = scala.collection.mutable.Shrinkable[A]
diff --git a/hail/hail/utils/src/is/hail/collection/AnyRefArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/AnyRefArrayBuilder.scala
new file mode 100644
index 00000000000..4d44c296de2
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/AnyRefArrayBuilder.scala
@@ -0,0 +1,78 @@
+package is.hail.collection
+
+import scala.reflect.ClassTag
+
+final class AnyRefArrayBuilder[T <: AnyRef](initialCapacity: Int = 16)(implicit ct: ClassTag[T]) {
+
+  var size_ : Int = 0
+  var b: Array[T] = new Array[T](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): T = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[T](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def add(x: T): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def +=(x: T): Unit = add(x)
+
+  def update(i: Int, x: T): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[T] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[T](initialCapacity)
+  }
+
+  def appendFrom(ab2: AnyRefArrayBuilder[T]): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): T = {
+    size_ -= 1
+    b(size)
+  }
+
+  def clearAndSetNull(): Unit = {
+    clear()
+    var i = 0
+    while (i < b.length) {
+      b(i) = (null.asInstanceOf[T])
+      i += 1
+    }
+  }
+
+  def setSizeUninitialized(size: Int): Unit = {
+    ensureCapacity(size)
+    size_ = size
+  }
+}
diff --git a/hail/hail/src/is/hail/utils/ArrayStack.scala b/hail/hail/utils/src/is/hail/collection/ArrayStack.scala
similarity index 97%
rename from hail/hail/src/is/hail/utils/ArrayStack.scala
rename to hail/hail/utils/src/is/hail/collection/ArrayStack.scala
index 3ee6131745a..cf2b82c5228 100644
--- a/hail/hail/src/is/hail/utils/ArrayStack.scala
+++ b/hail/hail/utils/src/is/hail/collection/ArrayStack.scala
@@ -1,4 +1,6 @@
-package is.hail.utils
+package is.hail.collection
+
+import is.hail.utils.uninitialized
 
 import scala.reflect.ClassTag
 
diff --git a/hail/hail/src/is/hail/utils/BinaryHeap.scala b/hail/hail/utils/src/is/hail/collection/BinaryHeap.scala
similarity index 99%
rename from hail/hail/src/is/hail/utils/BinaryHeap.scala
rename to hail/hail/utils/src/is/hail/collection/BinaryHeap.scala
index c12aad44f31..28087e208df 100644
--- a/hail/hail/src/is/hail/utils/BinaryHeap.scala
+++ b/hail/hail/utils/src/is/hail/collection/BinaryHeap.scala
@@ -1,4 +1,6 @@
-package is.hail.utils
+package is.hail.collection
+
+import is.hail.utils.fatal
 
 import scala.collection.mutable
 import scala.reflect.ClassTag
diff --git a/hail/hail/utils/src/is/hail/collection/BooleanArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/BooleanArrayBuilder.scala
new file mode 100644
index 00000000000..e90193cb3a0
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/BooleanArrayBuilder.scala
@@ -0,0 +1,62 @@
+package is.hail.collection
+
+final class BooleanArrayBuilder(initialCapacity: Int = 16) {
+
+  var size_ : Int = 0
+  var b: Array[Boolean] = new Array[Boolean](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): Boolean = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[Boolean](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def +=(x: Boolean) = add(x)
+
+  def add(x: Boolean): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Boolean): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Boolean] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[Boolean](initialCapacity)
+  }
+
+  def appendFrom(ab2: BooleanArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): Boolean = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/utils/src/is/hail/collection/ByteArrayArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/ByteArrayArrayBuilder.scala
new file mode 100644
index 00000000000..2d6c65c1f6c
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/ByteArrayArrayBuilder.scala
@@ -0,0 +1,43 @@
+package is.hail.collection
+
+final class ByteArrayArrayBuilder(initialCapacity: Int) {
+
+  var size_ : Int = 0
+  private var b: Array[Array[Byte]] = new Array[Array[Byte]](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): Array[Byte] = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[Array[Byte]](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def add(x: Array[Byte]): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Array[Byte]): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Array[Byte]] = b.slice(0, size_)
+}
diff --git a/hail/hail/utils/src/is/hail/collection/ByteArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/ByteArrayBuilder.scala
new file mode 100644
index 00000000000..8f2d08fa9c8
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/ByteArrayBuilder.scala
@@ -0,0 +1,79 @@
+package is.hail.collection
+
+final class ByteArrayBuilder(initialCapacity: Int = 16) {
+
+  var size_ : Int = 0
+  var b: Array[Byte] = new Array[Byte](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def setSizeUnchecked(n: Int): Unit =
+    size_ = n
+
+  def apply(i: Int): Byte = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[Byte](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def +=(x: Byte) = add(x)
+
+  def ++=(xs: Array[Byte]) = {
+    val newLen = size + xs.length
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, xs.length)
+    size_ = newLen
+  }
+
+  def ++=(xs: Array[Byte], n: Int) = {
+    val newLen = size + n
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, n)
+    size_ = newLen
+  }
+
+  def add(x: Byte): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Byte): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Byte] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[Byte](initialCapacity)
+  }
+
+  def appendFrom(ab2: ByteArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): Byte = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/utils/src/is/hail/collection/DoubleArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/DoubleArrayBuilder.scala
new file mode 100644
index 00000000000..25f73c9f1a9
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/DoubleArrayBuilder.scala
@@ -0,0 +1,81 @@
+package is.hail.collection
+
+final class DoubleArrayBuilder(initialCapacity: Int = 16) {
+
+  var size_ : Int = 0
+  var b: Array[Double] = new Array[Double](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): Double = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[Double](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def setSizeUninitialized(n: Int) = {
+    ensureCapacity(n)
+    size_ = n
+  }
+
+  def +=(x: Double): Unit = add(x)
+
+  def ++=(xs: Array[Double]) = {
+    val newLen = size + xs.length
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, xs.length)
+    size_ = newLen
+  }
+
+  def ++=(xs: Array[Double], n: Int) = {
+    val newLen = size + n
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, n)
+    size_ = newLen
+  }
+
+  def add(x: Double): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Double): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Double] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[Double](initialCapacity)
+  }
+
+  def appendFrom(ab2: DoubleArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): Double = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/src/is/hail/utils/FastSeq.scala b/hail/hail/utils/src/is/hail/collection/FastSeq.scala
similarity index 60%
rename from hail/hail/src/is/hail/utils/FastSeq.scala
rename to hail/hail/utils/src/is/hail/collection/FastSeq.scala
index fa56de498d0..21d5846bf2a 100644
--- a/hail/hail/src/is/hail/utils/FastSeq.scala
+++ b/hail/hail/utils/src/is/hail/collection/FastSeq.scala
@@ -1,9 +1,11 @@
-package is.hail.utils
+package is.hail.collection
+
+import is.hail.collection.implicits.toRichIterable
 
 import scala.reflect.ClassTag
 
 object FastSeq {
-  def empty[T: ClassTag]: IndexedSeq[T] =
+  def empty[T]: IndexedSeq[T] =
     IndexedSeq.empty
 
   def apply[T: ClassTag](args: T*): IndexedSeq[T] =
diff --git a/hail/hail/src/is/hail/utils/FlipbookIterator.scala b/hail/hail/utils/src/is/hail/collection/FlipbookIterator.scala
similarity index 88%
rename from hail/hail/src/is/hail/utils/FlipbookIterator.scala
rename to hail/hail/utils/src/is/hail/collection/FlipbookIterator.scala
index fe27fbf4481..1fb911feb6e 100644
--- a/hail/hail/src/is/hail/utils/FlipbookIterator.scala
+++ b/hail/hail/utils/src/is/hail/collection/FlipbookIterator.scala
@@ -1,9 +1,10 @@
-package is.hail.utils
+package is.hail.collection
 
-import is.hail.utils.compat.mutable.Growable
+import is.hail.collection.compat.mutable.Growable
+import is.hail.collection.implicits.toRichIterator
+import is.hail.utils.{Muple, OrderingView}
 
 import scala.collection.{mutable, BufferedIterator}
-import scala.collection.compat._
 import scala.reflect.ClassTag
 
 import org.typelevel.scalaccompat.annotation.nowarn213
@@ -31,8 +32,8 @@ abstract class StateMachine[A] {
 object StateMachine {
   def terminal[A]: StateMachine[A] = new StateMachine[A] {
     val isValid = false
-    def value: A = ???
-    def advance(): Unit = {}
+    override def value: A = ???
+    override def advance(): Unit = {}
   }
 }
 
@@ -45,10 +46,10 @@ class StagingIterator[A] private (sm: StateMachine[A]) extends FlipbookIterator[
   private var isConsumed: Boolean = false
 
   // FlipbookIterator interface
-  def isValid: Boolean = sm.isValid
-  def value: A = { assert(isValid && !isConsumed); sm.value }
+  override def isValid: Boolean = sm.isValid
+  override def value: A = { assert(isValid && !isConsumed); sm.value }
 
-  def advance(): Unit = {
+  override def advance(): Unit = {
     assert(isValid)
     isConsumed = false
     sm.advance()
@@ -67,21 +68,21 @@ class StagingIterator[A] private (sm: StateMachine[A]) extends FlipbookIterator[
 
   // (Buffered)Iterator interface, not intended to be used directly, only for
   // passing a StagingIterator where an Iterator is expected
-  def head: A = { stage(); sm.value }
+  override def head: A = { stage(); sm.value }
 
-  def hasNext: Boolean =
+  override def hasNext: Boolean =
     if (isValid) {
       stage()
       isValid
     } else false
 
-  def next(): A = {
+  override def next(): A = {
     stage()
     assert(isValid)
     consume()
   }
 
-  def toStagingIterator: StagingIterator[A] = this
+  override def toStagingIterator: StagingIterator[A] = this
 }
 
 object FlipbookIterator {
@@ -95,7 +96,7 @@ object FlipbookIterator {
     ord: (A, A) => Int,
   ): FlipbookIterator[collection.IndexedSeq[(A, Int)]] = {
     object TmpOrd extends Ordering[(A, Int)] {
-      def compare(x: (A, Int), y: (A, Int)): Int = ord(y._1, x._1)
+      override def compare(x: (A, Int), y: (A, Int)): Int = ord(y._1, x._1)
     }
     val sm = new StateMachine[collection.IndexedSeq[(A, Int)]] {
       val q: mutable.PriorityQueue[(A, Int)] = new mutable.PriorityQueue()(TmpOrd)
@@ -109,7 +110,7 @@ object FlipbookIterator {
         i += 1
       }
 
-      def advance(): Unit = {
+      override def advance(): Unit = {
         var i = 0
         while (i < value.length) {
           val j = value(i)._2
@@ -158,10 +159,10 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
 
   override def filter(pred: A => Boolean): FlipbookIterator[A] = FlipbookIterator(
     new StateMachine[A] {
-      def value = self.value
-      def isValid = self.isValid
+      override def value = self.value
+      override def isValid = self.isValid
 
-      def advance(): Unit =
+      override def advance(): Unit =
         do self.advance() while (self.isValid && !pred(self.value))
 
       while (self.isValid && !pred(self.value)) self.advance()
@@ -174,9 +175,9 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
     new StateMachine[B] {
       var value: B = _
       if (self.isValid) value = f(self.value)
-      def isValid = self.isValid
+      override def isValid = self.isValid
 
-      def advance(): Unit = {
+      override def advance(): Unit = {
         self.advance()
         if (self.isValid) value = f(self.value)
       }
@@ -184,16 +185,17 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
   )
 
   @nowarn213("msg=GenTraversableOnce in package collection is deprecated")
+  @nowarn213("msg=toIterator in class IterableOnceExtensionMethods is deprecated")
   override def flatMap[B](f: A => scala.collection.GenTraversableOnce[B]): FlipbookIterator[B] =
     FlipbookIterator(
       new StateMachine[B] {
         var it: FlipbookIterator[B] = _
         if (self.isValid) it = f(self.value).toIterator.toFlipbookIterator
         findNextValid()
-        def value: B = it.value
-        def isValid = self.isValid
+        override def value: B = it.value
+        override def isValid = self.isValid
 
-        def advance(): Unit = {
+        override def advance(): Unit = {
           it.advance()
           findNextValid()
         }
@@ -208,23 +210,23 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
 
   private[this] trait ValidityCachingStateMachine extends StateMachine[A] {
     private[this] var _isValid: Boolean = _
-    final def isValid = _isValid
+    final override def isValid = _isValid
 
     final def refreshValidity(): Unit =
       _isValid = calculateValidity
 
     def calculateValidity: Boolean
-    def value: A
-    def advance(): Unit
+    override def value: A
+    override def advance(): Unit
     refreshValidity()
   }
 
   def staircased(ord: OrderingView[A]): StagingIterator[FlipbookIterator[A]] = {
     ord.setBottom()
     val stepSM = new ValidityCachingStateMachine {
-      def value: A = self.value
-      def calculateValidity: Boolean = self.isValid && ord.isEquivalent(self.value)
-      def advance() = {
+      override def value: A = self.value
+      override def calculateValidity: Boolean = self.isValid && ord.isEquivalent(self.value)
+      override def advance() = {
         self.advance()
         refreshValidity()
       }
@@ -233,7 +235,7 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
     val sm = new StateMachine[FlipbookIterator[A]] {
       var isValid: Boolean = true
       val value: FlipbookIterator[A] = stepIterator
-      def advance() = {
+      override def advance() = {
         stepIterator.exhaust()
         if (self.isValid) {
           ord.setValue(self.value)
@@ -275,7 +277,7 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
     val sm = new StateMachine[Muple[A, B]] {
       val value = Muple(leftDefault, rightDefault)
       var isValid = true
-      def advance(): Unit = {
+      override def advance(): Unit = {
         left.stage()
         right.stage()
         val c = {
@@ -341,7 +343,7 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
         }
       }
 
-      def advance(): Unit = {
+      override def advance(): Unit = {
         left.advance()
         setValue()
       }
@@ -439,7 +441,7 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
     class MergeStateMachine extends StateMachine[A] {
       var value: A = _
       var isValid = true
-      def advance(): Unit = {
+      override def advance(): Unit = {
         left.stage()
         right.stage()
         val c = {
@@ -475,7 +477,7 @@ abstract class FlipbookIterator[A] extends BufferedIterator[A] { self =>
 
   // head, next, and hasNext are not meant to be used directly, only to enable
   // FlipbookIterator to be used where an Iterator is expected.
-  def head: A
-  def next(): A
-  def hasNext: Boolean
+  override def head: A
+  override def next(): A
+  override def hasNext: Boolean
 }
diff --git a/hail/hail/src/is/hail/utils/ImmutableMap.scala b/hail/hail/utils/src/is/hail/collection/ImmutableMap.scala
similarity index 85%
rename from hail/hail/src/is/hail/utils/ImmutableMap.scala
rename to hail/hail/utils/src/is/hail/collection/ImmutableMap.scala
index 96eee16fe07..ec1d833f95b 100644
--- a/hail/hail/src/is/hail/utils/ImmutableMap.scala
+++ b/hail/hail/utils/src/is/hail/collection/ImmutableMap.scala
@@ -1,6 +1,6 @@
-package is.hail.utils
+package is.hail.collection
 
-import is.hail.utils.compat.mutable.{GrowableCompat, ShrinkableCompat}
+import is.hail.collection.compat.mutable.{GrowableCompat, ShrinkableCompat}
 
 import scala.collection.mutable
 
diff --git a/hail/hail/utils/src/is/hail/collection/IntArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/IntArrayBuilder.scala
new file mode 100644
index 00000000000..0b02195e6a7
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/IntArrayBuilder.scala
@@ -0,0 +1,81 @@
+package is.hail.collection
+
+final class IntArrayBuilder(initialCapacity: Int = 16) {
+
+  var size_ : Int = 0
+  var b: Array[Int] = new Array[Int](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): Int = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[Int](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def setSizeUninitialized(n: Int) = {
+    ensureCapacity(n)
+    size_ = n
+  }
+
+  def +=(x: Int): Unit = add(x)
+
+  def ++=(xs: Array[Int]) = {
+    val newLen = size + xs.length
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, xs.length)
+    size_ = newLen
+  }
+
+  def ++=(xs: Array[Int], n: Int) = {
+    val newLen = size + n
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, n)
+    size_ = newLen
+  }
+
+  def add(x: Int): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Int): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Int] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[Int](initialCapacity)
+  }
+
+  def appendFrom(ab2: IntArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): Int = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/utils/src/is/hail/collection/LongArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/LongArrayBuilder.scala
new file mode 100644
index 00000000000..1e8ccbf2f3e
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/LongArrayBuilder.scala
@@ -0,0 +1,76 @@
+package is.hail.collection
+
+final class LongArrayBuilder(initialCapacity: Int = 16) {
+
+  var size_ : Int = 0
+  var b: Array[Long] = new Array[Long](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): Long = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, (b.length * 2))
+      val newb = new Array[Long](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def +=(x: Long): Unit = add(x)
+
+  def ++=(xs: Array[Long]) = {
+    val newLen = size + xs.length
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, xs.length)
+    size_ = newLen
+  }
+
+  def ++=(xs: Array[Long], n: Int) = {
+    val newLen = size + n
+    ensureCapacity(newLen)
+    System.arraycopy(xs, 0, b, size_, n)
+    size_ = newLen
+  }
+
+  def add(x: Long): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: Long): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[Long] = b.slice(0, size_)
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[Long](initialCapacity)
+  }
+
+  def appendFrom(ab2: LongArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): Long = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/src/is/hail/utils/MissingArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/MissingArrayBuilder.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/MissingArrayBuilder.scala
rename to hail/hail/utils/src/is/hail/collection/MissingArrayBuilder.scala
index 8b18e5f7f78..b389c4d46d3 100644
--- a/hail/hail/src/is/hail/utils/MissingArrayBuilder.scala
+++ b/hail/hail/utils/src/is/hail/collection/MissingArrayBuilder.scala
@@ -1,4 +1,4 @@
-package is.hail.utils
+package is.hail.collection
 
 import scala.reflect.ClassTag
 
diff --git a/hail/hail/utils/src/is/hail/collection/StringArrayBuilder.scala b/hail/hail/utils/src/is/hail/collection/StringArrayBuilder.scala
new file mode 100644
index 00000000000..0670f0598d1
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/StringArrayBuilder.scala
@@ -0,0 +1,65 @@
+package is.hail.collection
+
+final class StringArrayBuilder(initialCapacity: Int = 16) {
+  var size_ : Int = 0
+  var b: Array[String] = new Array[String](initialCapacity)
+
+  def size: Int = size_
+
+  def setSize(n: Int): Unit = {
+    require(n >= 0 && n <= size)
+    size_ = n
+  }
+
+  def apply(i: Int): String = {
+    require(i >= 0 && i < size)
+    b(i)
+  }
+
+  def ensureCapacity(n: Int): Unit = {
+    if (b.length < n) {
+      val newCapacity = math.max(n, b.length * 2)
+      val newb = new Array[String](newCapacity)
+      Array.copy(b, 0, newb, 0, size_)
+      b = newb
+    }
+  }
+
+  def +=(x: String) = add(x)
+
+  def add(x: String): Unit = {
+    ensureCapacity(size_ + 1)
+    b(size_) = x
+    size_ += 1
+  }
+
+  def update(i: Int, x: String): Unit = {
+    require(i >= 0 && i < size)
+    b(i) = x
+  }
+
+  def clear(): Unit = size_ = 0
+
+  def result(): Array[String] = {
+    val a = new Array[String](size_)
+    System.arraycopy(b, 0, a, 0, size_)
+    a
+  }
+
+  def clearAndResize(): Unit = {
+    size_ = 0
+    if (b.length > initialCapacity)
+      b = new Array[String](initialCapacity)
+  }
+
+  def appendFrom(ab2: StringArrayBuilder): Unit = {
+    ensureCapacity(size_ + ab2.size_)
+    System.arraycopy(ab2.b, 0, b, size_, ab2.size_)
+    size_ = size_ + ab2.size_
+  }
+
+  def pop(): String = {
+    size_ -= 1
+    b(size)
+  }
+}
diff --git a/hail/hail/utils/src/is/hail/collection/implicits/RichArray.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichArray.scala
new file mode 100644
index 00000000000..66147af8562
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichArray.scala
@@ -0,0 +1,5 @@
+package is.hail.collection.implicits
+
+class RichArray[T](val a: Array[T]) extends AnyVal {
+  def index: Map[T, Int] = a.zipWithIndex.toMap
+}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichArraySeq.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichArraySeqCompanion.scala
similarity index 85%
rename from hail/hail/src/is/hail/utils/richUtils/RichArraySeq.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichArraySeqCompanion.scala
index b81736204ad..f110ac6de70 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichArraySeq.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichArraySeqCompanion.scala
@@ -1,7 +1,7 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.collection.compat._
+import is.hail.collection.compat.immutable.ArraySeq
 
 import scala.collection.mutable
 import scala.reflect.ClassTag
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichIndexedSeq.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichIndexedSeq.scala
similarity index 99%
rename from hail/hail/src/is/hail/utils/richUtils/RichIndexedSeq.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichIndexedSeq.scala
index 4d1e7e7c4b4..a406e9a6133 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichIndexedSeq.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichIndexedSeq.scala
@@ -1,6 +1,4 @@
-package is.hail.utils.richUtils
-
-import is.hail.utils._
+package is.hail.collection.implicits
 
 import scala.reflect.ClassTag
 
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichIterable.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichIterable.scala
similarity index 75%
rename from hail/hail/src/is/hail/utils/richUtils/RichIterable.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichIterable.scala
index ab8f956d3d6..3b93763aae0 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichIterable.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichIterable.scala
@@ -1,14 +1,11 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
+import is.hail.collection.compat.immutable.ArraySeq
 import is.hail.utils._
-import is.hail.utils.compat._
-import is.hail.utils.compat.immutable.ArraySeq
 
 import scala.collection.{mutable, AbstractIterable}
 import scala.reflect.ClassTag
 
-import java.io.Serializable
-
 object RichIterable {
   def single[A](a: A): Iterable[A] = new AbstractIterable[A] {
     override def iterator = Iterator.single(a)
@@ -30,40 +27,40 @@ class RichIterable[T](val i: Iterable[T]) extends Serializable {
     i.iterator.foreachBetween(f)(g)
 
   def intersperse[S >: T](sep: S): Iterable[S] = new Iterable[S] {
-    def iterator = i.iterator.intersperse(sep)
+    override def iterator = i.iterator.intersperse(sep)
   }
 
   def intersperse[S >: T](start: S, sep: S, end: S): Iterable[S] = new Iterable[S] {
-    def iterator = i.iterator.intersperse(start, sep, end)
+    override def iterator = i.iterator.intersperse(start, sep, end)
   }
 
   def +:[S >: T](elt: S): Iterable[S] = new Iterable[S] {
-    def iterator = Iterator.single(elt) ++ i
+    override def iterator = Iterator.single(elt) ++ i
   }
 
   def lazyMapWith[T2, S](i2: Iterable[T2], f: (T, T2) => S): Iterable[S] =
     new Iterable[S] with Serializable {
-      def iterator: Iterator[S] = new Iterator[S] {
+      override def iterator: Iterator[S] = new Iterator[S] {
         val it: Iterator[T] = i.iterator
         val it2: Iterator[T2] = i2.iterator
 
-        def hasNext: Boolean = it.hasNext && it2.hasNext
+        override def hasNext: Boolean = it.hasNext && it2.hasNext
 
-        def next(): S = f(it.next(), it2.next())
+        override def next(): S = f(it.next(), it2.next())
       }
     }
 
   def lazyMapWith2[T2, T3, S](i2: Iterable[T2], i3: Iterable[T3], f: (T, T2, T3) => S)
     : Iterable[S] =
     new Iterable[S] with Serializable {
-      def iterator: Iterator[S] = new Iterator[S] {
+      override def iterator: Iterator[S] = new Iterator[S] {
         val it: Iterator[T] = i.iterator
         val it2: Iterator[T2] = i2.iterator
         val it3: Iterator[T3] = i3.iterator
 
-        def hasNext: Boolean = it.hasNext && it2.hasNext && it3.hasNext
+        override def hasNext: Boolean = it.hasNext && it2.hasNext && it3.hasNext
 
-        def next(): S = f(it.next(), it2.next(), it3.next())
+        override def next(): S = f(it.next(), it2.next(), it3.next())
       }
     }
 
@@ -89,12 +86,12 @@ class RichIterable[T](val i: Iterable[T]) extends Serializable {
   }
 
   def truncatable(delim: String = ", ", toTake: Int = 10): Truncatable = new Truncatable {
-    def truncate: String = if (i.size > toTake)
+    override def truncate: String = if (i.size > toTake)
       i.take(toTake).mkString(delim) + delim + "..."
     else
       i.mkString(delim)
 
-    def strings: (String, String) = (truncate, i.mkString(delim))
+    override def strings: (String, String) = (truncate, i.mkString(delim))
   }
 
   def counter(): Map[T, Int] = {
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichIterator.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichIterator.scala
similarity index 76%
rename from hail/hail/src/is/hail/utils/richUtils/RichIterator.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichIterator.scala
index c910abb604c..83f8f44db6b 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichIterator.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichIterator.scala
@@ -1,8 +1,6 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
-import is.hail.annotations.{Region, RegionValue}
-import is.hail.types.physical.PStruct
-import is.hail.utils.{FlipbookIterator, StagingIterator, StateMachine}
+import is.hail.collection.{FlipbookIterator, StagingIterator, StateMachine}
 
 import scala.io.Source
 import scala.jdk.CollectionConverters._
@@ -10,23 +8,14 @@ import scala.reflect.ClassTag
 
 import java.io.PrintWriter
 
-import org.apache.spark.sql.Row
-
-class RichIteratorLong(val it: Iterator[Long]) extends AnyVal {
-  def toIteratorRV(region: Region): Iterator[RegionValue] = {
-    val rv = RegionValue(region)
-    it.map { ptr => rv.setOffset(ptr); rv }
-  }
-}
-
 class RichIterator[T](val it: Iterator[T]) extends AnyVal {
   def toStagingIterator: StagingIterator[T] = {
     val bit = it.buffered
     StagingIterator(
       new StateMachine[T] {
-        def value: T = bit.head
-        def isValid = bit.hasNext
-        def advance(): Unit = bit.next(): Unit
+        override def value: T = bit.head
+        override def isValid = bit.hasNext
+        override def advance(): Unit = bit.next(): Unit
       }
     )
   }
@@ -45,9 +34,9 @@ class RichIterator[T](val it: Iterator[T]) extends AnyVal {
 
   def intersperse[S >: T](sep: S): Iterator[S] = new Iterator[S] {
     var nextIsSep = false
-    def hasNext = it.hasNext
+    override def hasNext = it.hasNext
 
-    def next() = {
+    override def next() = {
       val n = if (nextIsSep) sep else it.next()
       nextIsSep = !nextIsSep
       n
@@ -56,9 +45,9 @@ class RichIterator[T](val it: Iterator[T]) extends AnyVal {
 
   def intersperse[S >: T](start: S, sep: S, end: S): Iterator[S] = new Iterator[S] {
     var state = 0
-    def hasNext = state != 4
+    override def hasNext = state != 4
 
-    def next() = {
+    override def next() = {
       state match {
         case 0 =>
           state = if (it.hasNext) 1 else 3
@@ -117,9 +106,9 @@ class RichIterator[T](val it: Iterator[T]) extends AnyVal {
     new Iterator[Iterator[T]] {
       var prev: Iterator[T] = null
 
-      def hasNext: Boolean = it.hasNext
+      override def hasNext: Boolean = it.hasNext
 
-      def next(): Iterator[T] = {
+      override def next(): Iterator[T] = {
         if (!hasNext)
           throw new NoSuchElementException("next on empty iterator")
 
@@ -129,9 +118,9 @@ class RichIterator[T](val it: Iterator[T]) extends AnyVal {
         prev = new Iterator[T] {
           var i = 0
 
-          def hasNext: Boolean = it.hasNext && i < groupSize
+          override def hasNext: Boolean = it.hasNext && i < groupSize
 
-          def next(): T = {
+          override def next(): T = {
             if (!hasNext)
               throw new NoSuchElementException("next on empty iterator")
             i += 1
@@ -147,8 +136,3 @@ class RichIterator[T](val it: Iterator[T]) extends AnyVal {
 
   def headOption: Option[T] = if (it.isEmpty) None else Some(it.next())
 }
-
-class RichRowIterator(val it: Iterator[Row]) extends AnyVal {
-  def copyToRegion(region: Region, rowTyp: PStruct): Iterator[Long] =
-    it.map(row => rowTyp.unstagedStoreJavaObject(null, row, region))
-}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichMap.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichMap.scala
similarity index 91%
rename from hail/hail/src/is/hail/utils/richUtils/RichMap.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichMap.scala
index 5d080063e74..d9c3ca51a6a 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichMap.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichMap.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
 class RichMap[K, V](val m: Map[K, V]) extends AnyVal {
   def force =
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichMutableMap.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichMutableMap.scala
similarity index 84%
rename from hail/hail/src/is/hail/utils/richUtils/RichMutableMap.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichMutableMap.scala
index 11c258d142d..24caa8b3e56 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichMutableMap.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichMutableMap.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
 import scala.collection.mutable
 
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichOption.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichOption.scala
similarity index 88%
rename from hail/hail/src/is/hail/utils/richUtils/RichOption.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichOption.scala
index 2cd23662698..382528ad523 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichOption.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichOption.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
 class RichOption[T](val o: Option[T]) extends AnyVal {
   def contains(v: T): Boolean = o.isDefined && o.get == v
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichOrderedArray.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichOrderedArray.scala
similarity index 72%
rename from hail/hail/src/is/hail/utils/richUtils/RichOrderedArray.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichOrderedArray.scala
index ee00c0cc39c..42d25eb83f0 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichOrderedArray.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichOrderedArray.scala
@@ -1,6 +1,4 @@
-package is.hail.utils.richUtils
-
-import is.hail.utils._
+package is.hail.collection.implicits
 
 class RichOrderedArray[T: Ordering](a: Array[T]) {
   def isIncreasing: Boolean = a.toSeq.isIncreasing
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichOrderedSeq.scala b/hail/hail/utils/src/is/hail/collection/implicits/RichOrderedSeq.scala
similarity index 90%
rename from hail/hail/src/is/hail/utils/richUtils/RichOrderedSeq.scala
rename to hail/hail/utils/src/is/hail/collection/implicits/RichOrderedSeq.scala
index 20d149bc0e5..b0652cde815 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichOrderedSeq.scala
+++ b/hail/hail/utils/src/is/hail/collection/implicits/RichOrderedSeq.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.collection.implicits
 
 import scala.collection.compat._
 
diff --git a/hail/hail/utils/src/is/hail/collection/implicits/package.scala b/hail/hail/utils/src/is/hail/collection/implicits/package.scala
new file mode 100644
index 00000000000..09caf67fe52
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/collection/implicits/package.scala
@@ -0,0 +1,39 @@
+package is.hail.collection
+
+import is.hail.collection.compat.immutable.ArraySeq
+
+import scala.collection.mutable
+
+package object implicits {
+  implicit def toRichArray[T](a: Array[T]): RichArray[T] = new RichArray(a)
+
+  implicit def toRichArraySeqCompanion(a: ArraySeq.type): RichArraySeqCompanion.type =
+    RichArraySeqCompanion
+
+  implicit def toRichIndexedSeq[T](s: IndexedSeq[T]): RichIndexedSeq[T] = new RichIndexedSeq(s)
+
+  implicit def toRichIndexedSeqAnyRef[T <: AnyRef](s: IndexedSeq[T]): RichIndexedSeqAnyRef[T] =
+    new RichIndexedSeqAnyRef(s)
+
+  implicit def arrayToRichIndexedSeq[T](s: Array[T]): RichIndexedSeq[T] = new RichIndexedSeq(s)
+
+  implicit def toRichIterable[T](i: Iterable[T]): RichIterable[T] = new RichIterable(i)
+
+  implicit def toRichIterable[T](a: Array[T]): RichIterable[T] = new RichIterable(a)
+
+  implicit def toRichIterator[T](it: Iterator[T]): RichIterator[T] = new RichIterator[T](it)
+
+  implicit def toRichMap[K, V](m: Map[K, V]): RichMap[K, V] = new RichMap(m)
+
+  implicit def toRichMutableMap[K, V](m: mutable.Map[K, V]): RichMutableMap[K, V] =
+    new RichMutableMap(m)
+
+  implicit def toRichOption[T](o: Option[T]): RichOption[T] = new RichOption[T](o)
+
+  implicit def toRichOrderedArray[T: Ordering](a: Array[T]): RichOrderedArray[T] =
+    new RichOrderedArray(a)
+
+  implicit def toRichOrderedSeq[T: Ordering](s: Seq[T]): RichOrderedSeq[T] =
+    new RichOrderedSeq[T](s)
+
+}
diff --git a/hail/hail/src/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala b/hail/hail/utils/src/is/hail/utils/ArrayOfByteArrayInputStream.scala
similarity index 97%
rename from hail/hail/src/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala
rename to hail/hail/utils/src/is/hail/utils/ArrayOfByteArrayInputStream.scala
index 1526bf96b7a..fac9b97fad1 100644
--- a/hail/hail/src/is/hail/utils/prettyPrint/ArrayOfByteArrayInputStream.scala
+++ b/hail/hail/utils/src/is/hail/utils/ArrayOfByteArrayInputStream.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.prettyPrint
+package is.hail.utils
 
 import java.io.{ByteArrayInputStream, InputStream}
 
diff --git a/hail/hail/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala b/hail/hail/utils/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala
rename to hail/hail/utils/src/is/hail/utils/ArrayOfByteArrayOutputStream.scala
diff --git a/hail/hail/src/is/hail/utils/BufferedAggregatorIterator.scala b/hail/hail/utils/src/is/hail/utils/BufferedAggregatorIterator.scala
similarity index 92%
rename from hail/hail/src/is/hail/utils/BufferedAggregatorIterator.scala
rename to hail/hail/utils/src/is/hail/utils/BufferedAggregatorIterator.scala
index 7190686b520..02d51b0129f 100644
--- a/hail/hail/src/is/hail/utils/BufferedAggregatorIterator.scala
+++ b/hail/hail/utils/src/is/hail/utils/BufferedAggregatorIterator.scala
@@ -1,5 +1,7 @@
 package is.hail.utils
 
+import is.hail.collection.implicits.toRichIterator
+
 import java.util
 
 object BufferedAggregatorIterator {
@@ -31,10 +33,10 @@ class BufferedAggregatorIterator[T, V, U, K](
       } else false
   }
 
-  def hasNext: Boolean =
+  override def hasNext: Boolean =
     fb.isValid || buffer.size() > 0
 
-  def next(): (K, U) = {
+  override def next(): (K, U) = {
     if (!hasNext)
       throw new NoSuchElementException
     while (fb.isValid) {
diff --git a/hail/hail/src/is/hail/utils/BytePacker.scala b/hail/hail/utils/src/is/hail/utils/BytePacker.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/BytePacker.scala
rename to hail/hail/utils/src/is/hail/utils/BytePacker.scala
diff --git a/hail/hail/src/is/hail/utils/CompressionUtils.scala b/hail/hail/utils/src/is/hail/utils/CompressionUtils.scala
similarity index 97%
rename from hail/hail/src/is/hail/utils/CompressionUtils.scala
rename to hail/hail/utils/src/is/hail/utils/CompressionUtils.scala
index 312e6b61e33..8c0669b59bd 100644
--- a/hail/hail/src/is/hail/utils/CompressionUtils.scala
+++ b/hail/hail/utils/src/is/hail/utils/CompressionUtils.scala
@@ -1,6 +1,6 @@
 package is.hail.utils
 
-import is.hail.expr.ir.ByteArrayBuilder
+import is.hail.collection.ByteArrayBuilder
 
 import java.util.zip.{Deflater, Inflater}
 
diff --git a/hail/hail/src/is/hail/utils/Context.scala b/hail/hail/utils/src/is/hail/utils/Context.scala
similarity index 96%
rename from hail/hail/src/is/hail/utils/Context.scala
rename to hail/hail/utils/src/is/hail/utils/Context.scala
index 2dbbcfcc77d..d514babf900 100644
--- a/hail/hail/src/is/hail/utils/Context.scala
+++ b/hail/hail/utils/src/is/hail/utils/Context.scala
@@ -1,5 +1,7 @@
 package is.hail.utils
 
+import is.hail.utils.implicits.toTruncatable
+
 case class Context(line: String, file: String, position: Option[Int]) {
   def locationString: String =
     position match {
diff --git a/hail/hail/src/is/hail/utils/DateFormatUtils.scala b/hail/hail/utils/src/is/hail/utils/DateFormatUtils.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/DateFormatUtils.scala
rename to hail/hail/utils/src/is/hail/utils/DateFormatUtils.scala
diff --git a/hail/hail/src/is/hail/utils/ErrorHandling.scala b/hail/hail/utils/src/is/hail/utils/ErrorHandling.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/ErrorHandling.scala
rename to hail/hail/utils/src/is/hail/utils/ErrorHandling.scala
diff --git a/hail/hail/src/is/hail/utils/ExecutionTimer.scala b/hail/hail/utils/src/is/hail/utils/ExecutionTimer.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/ExecutionTimer.scala
rename to hail/hail/utils/src/is/hail/utils/ExecutionTimer.scala
index d96b0fb3b2d..4abfee589e2 100644
--- a/hail/hail/src/is/hail/utils/ExecutionTimer.scala
+++ b/hail/hail/utils/src/is/hail/utils/ExecutionTimer.scala
@@ -1,5 +1,6 @@
 package is.hail.utils
 
+import is.hail.collection.{FastSeq, ObjectArrayStack}
 import is.hail.utils.ExecutionTimer.{TimeBlock, Timings}
 
 import scala.collection.mutable
diff --git a/hail/hail/src/is/hail/utils/Logging.scala b/hail/hail/utils/src/is/hail/utils/Logging.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/Logging.scala
rename to hail/hail/utils/src/is/hail/utils/Logging.scala
diff --git a/hail/hail/src/is/hail/utils/Muple.scala b/hail/hail/utils/src/is/hail/utils/Muple.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/Muple.scala
rename to hail/hail/utils/src/is/hail/utils/Muple.scala
diff --git a/hail/hail/src/is/hail/utils/OrderingView.scala b/hail/hail/utils/src/is/hail/utils/OrderingView.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/OrderingView.scala
rename to hail/hail/utils/src/is/hail/utils/OrderingView.scala
diff --git a/hail/hail/src/is/hail/utils/ParseTrieNode.scala b/hail/hail/utils/src/is/hail/utils/ParseTrieNode.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/ParseTrieNode.scala
rename to hail/hail/utils/src/is/hail/utils/ParseTrieNode.scala
diff --git a/hail/hail/src/is/hail/utils/RestartableByteArrayInputStream.scala b/hail/hail/utils/src/is/hail/utils/RestartableByteArrayInputStream.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/RestartableByteArrayInputStream.scala
rename to hail/hail/utils/src/is/hail/utils/RestartableByteArrayInputStream.scala
diff --git a/hail/hail/src/is/hail/utils/SemanticVersion.scala b/hail/hail/utils/src/is/hail/utils/SemanticVersion.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/SemanticVersion.scala
rename to hail/hail/utils/src/is/hail/utils/SemanticVersion.scala
diff --git a/hail/hail/src/is/hail/utils/StackSafe.scala b/hail/hail/utils/src/is/hail/utils/StackSafe.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/StackSafe.scala
rename to hail/hail/utils/src/is/hail/utils/StackSafe.scala
diff --git a/hail/hail/src/is/hail/utils/StringEscapeUtils.scala b/hail/hail/utils/src/is/hail/utils/StringEscapeUtils.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/StringEscapeUtils.scala
rename to hail/hail/utils/src/is/hail/utils/StringEscapeUtils.scala
diff --git a/hail/hail/src/is/hail/utils/TextInputFilterAndReplace.scala b/hail/hail/utils/src/is/hail/utils/TextInputFilterAndReplace.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/TextInputFilterAndReplace.scala
rename to hail/hail/utils/src/is/hail/utils/TextInputFilterAndReplace.scala
diff --git a/hail/hail/src/is/hail/utils/Traceback.scala b/hail/hail/utils/src/is/hail/utils/Traceback.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/Traceback.scala
rename to hail/hail/utils/src/is/hail/utils/Traceback.scala
diff --git a/hail/hail/src/is/hail/utils/TreeTraversal.scala b/hail/hail/utils/src/is/hail/utils/TreeTraversal.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/TreeTraversal.scala
rename to hail/hail/utils/src/is/hail/utils/TreeTraversal.scala
diff --git a/hail/hail/src/is/hail/utils/TryAll.scala b/hail/hail/utils/src/is/hail/utils/TryAll.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/TryAll.scala
rename to hail/hail/utils/src/is/hail/utils/TryAll.scala
diff --git a/hail/hail/src/is/hail/utils/UnionFind.scala b/hail/hail/utils/src/is/hail/utils/UnionFind.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/UnionFind.scala
rename to hail/hail/utils/src/is/hail/utils/UnionFind.scala
diff --git a/hail/hail/src/is/hail/utils/richUtils/ByteTrackingOutputStream.scala b/hail/hail/utils/src/is/hail/utils/implicits/ByteTrackingOutputStream.scala
similarity index 86%
rename from hail/hail/src/is/hail/utils/richUtils/ByteTrackingOutputStream.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/ByteTrackingOutputStream.scala
index d8d89d4c99c..92f2cbc0e29 100644
--- a/hail/hail/src/is/hail/utils/richUtils/ByteTrackingOutputStream.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/ByteTrackingOutputStream.scala
@@ -1,11 +1,11 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 import java.io.OutputStream
 
 class ByteTrackingOutputStream(base: OutputStream) extends OutputStream {
   var bytesWritten = 0L
 
-  def write(c: Int): Unit = {
+  override def write(c: Int): Unit = {
     bytesWritten += 1
     base.write(c)
   }
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichBoolean.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichBoolean.scala
similarity index 91%
rename from hail/hail/src/is/hail/utils/richUtils/RichBoolean.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/RichBoolean.scala
index 5097faea98e..b23b0df3c30 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichBoolean.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichBoolean.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 class RichBoolean(val b: Boolean) extends AnyVal {
   def ==>(that: => Boolean): Boolean = !b || that
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichContextIterator.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichContextIterator.scala
similarity index 88%
rename from hail/hail/src/is/hail/utils/richUtils/RichContextIterator.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/RichContextIterator.scala
index 3e77555f642..b7437fefae6 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichContextIterator.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichContextIterator.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 import is.hail.utils.WithContext
 
diff --git a/hail/hail/utils/src/is/hail/utils/implicits/RichInputStream.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichInputStream.scala
new file mode 100644
index 00000000000..31c371a6b6b
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichInputStream.scala
@@ -0,0 +1,15 @@
+package is.hail.utils.implicits
+
+import is.hail.utils._
+
+import java.io.InputStream
+
+class RichInputStream(val in: InputStream) extends AnyVal {
+  def readFully(to: Array[Byte]): Unit =
+    readFully(to, 0, to.length)
+
+  def readFully(to: Array[Byte], toOff: Int, n: Int): Unit = {
+    val nRead = in.readNBytes(to, toOff, n)
+    if (nRead < n) fatal(s"Premature end of file: expected $n bytes, found $nRead")
+  }
+}
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichPartialKleisliOptionFunction.scala
similarity index 81%
rename from hail/hail/src/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/RichPartialKleisliOptionFunction.scala
index 3d5d6978ef4..8e5520ddfda 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichPartialKleisliOptionFunction.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichPartialKleisliOptionFunction.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 class RichPartialKleisliOptionFunction[A, B](pf: PartialFunction[A, Option[B]]) {
   def flatLift: A => Option[B] = a => pf.lift(a).flatten
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichPredicate.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichPredicate.scala
similarity index 89%
rename from hail/hail/src/is/hail/utils/richUtils/RichPredicate.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/RichPredicate.scala
index f0972728449..6f351c9a321 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichPredicate.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichPredicate.scala
@@ -1,4 +1,4 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 class RichPredicate[A](val f: A => Boolean) extends AnyVal {
   def and[B >: A](g: B => Boolean): A => Boolean =
diff --git a/hail/hail/src/is/hail/utils/richUtils/RichString.scala b/hail/hail/utils/src/is/hail/utils/implicits/RichString.scala
similarity index 69%
rename from hail/hail/src/is/hail/utils/richUtils/RichString.scala
rename to hail/hail/utils/src/is/hail/utils/implicits/RichString.scala
index e871170e64f..89aeeea7966 100644
--- a/hail/hail/src/is/hail/utils/richUtils/RichString.scala
+++ b/hail/hail/utils/src/is/hail/utils/implicits/RichString.scala
@@ -1,12 +1,12 @@
-package is.hail.utils.richUtils
+package is.hail.utils.implicits
 
 import is.hail.utils.Truncatable
 
 class RichString(val str: String) extends AnyVal {
   def truncatable(toTake: Int = 60): Truncatable = new Truncatable {
-    def truncate: String = if (str.length > toTake - 3) str.take(toTake) + "..." else str
+    override def truncate: String = if (str.length > toTake - 3) str.take(toTake) + "..." else str
 
-    def strings: (String, String) = (truncate, str)
+    override def strings: (String, String) = (truncate, str)
   }
 
   def equalsCaseInsensitive(other: String): Boolean =
diff --git a/hail/hail/utils/src/is/hail/utils/implicits/package.scala b/hail/hail/utils/src/is/hail/utils/implicits/package.scala
new file mode 100644
index 00000000000..af8d807fbc6
--- /dev/null
+++ b/hail/hail/utils/src/is/hail/utils/implicits/package.scala
@@ -0,0 +1,29 @@
+package is.hail.utils
+
+import is.hail.collection.implicits.toRichIterable
+
+import java.io.InputStream
+
+package object implicits {
+
+  implicit def toRichBoolean(b: Boolean): RichBoolean = new RichBoolean(b)
+
+  implicit def toRichContextIterator[T](it: Iterator[WithContext[T]]): RichContextIterator[T] =
+    new RichContextIterator[T](it)
+
+  implicit def toRichPredicate[A](f: A => Boolean): RichPredicate[A] = new RichPredicate[A](f)
+
+  implicit def toRichString(str: String): RichString = new RichString(str)
+
+  implicit def toTruncatable(s: String): Truncatable = s.truncatable()
+
+  implicit def toTruncatable[T](it: Iterable[T]): Truncatable = it.truncatable()
+
+  implicit def toTruncatable(arr: Array[_]): Truncatable = toTruncatable(arr: Iterable[_])
+
+  implicit def toRichInputStream(in: InputStream): RichInputStream = new RichInputStream(in)
+
+  implicit def toRichPartialKleisliOptionFunction[A, B](x: PartialFunction[A, Option[B]])
+    : RichPartialKleisliOptionFunction[A, B] = new RichPartialKleisliOptionFunction(x)
+
+}
diff --git a/hail/hail/src/is/hail/utils/package.scala b/hail/hail/utils/src/is/hail/utils/package.scala
similarity index 72%
rename from hail/hail/src/is/hail/utils/package.scala
rename to hail/hail/utils/src/is/hail/utils/package.scala
index 37535404e15..7653b70ab3e 100644
--- a/hail/hail/src/is/hail/utils/package.scala
+++ b/hail/hail/utils/src/is/hail/utils/package.scala
@@ -1,9 +1,8 @@
 package is.hail
 
-import is.hail.annotations.ExtendedOrdering
-import is.hail.expr.ir.ByteArrayBuilder
-import is.hail.io.fs.{FS, FileListEntry}
-import is.hail.utils.compat.immutable.ArraySeq
+import is.hail.collection.ByteArrayBuilder
+import is.hail.collection.compat.immutable.ArraySeq
+import is.hail.utils.implicits.toRichBoolean
 
 import scala.collection.compat._
 import scala.collection.mutable
@@ -15,27 +14,15 @@ import java.lang.reflect.Method
 import java.net.{URI, URLClassLoader}
 import java.nio.charset.StandardCharsets
 import java.security.SecureRandom
-import java.text.SimpleDateFormat
-import java.util.{Base64, Date}
-
-import org.apache.commons.lang3.StringUtils
-import org.apache.hadoop.fs.PathIOException
-import org.apache.hadoop.mapred.FileSplit
-import org.apache.hadoop.mapreduce.lib.input.{FileSplit => NewFileSplit}
-import org.apache.spark.{Partition, TaskContext}
-import org.apache.spark.sql.Row
-import org.json4s.{Extraction, Formats, JObject, JValue, NoTypeHints, Serializer}
-import org.json4s.JsonAST.{JArray, JString}
-import org.json4s.jackson.{JsonMethods, Serialization}
-import org.json4s.reflect.TypeInfo
+import java.util.Base64
 
-package utils {
-
-  import scala.collection.compat.{Factory, IterableOnce}
+import org.json4s.{Extraction, Formats, JObject, JValue}
+import org.json4s.JsonAST.JString
+import org.json4s.jackson.JsonMethods
 
+package utils {
   trait Truncatable {
     def truncate: String
-
     def strings: (String, String)
   }
 
@@ -53,7 +40,7 @@ package utils {
   sealed trait AnyFailAllFail[C[_]] {
     def apply[T](ts: IterableOnce[Option[T]])(implicit cbf: Factory[T, C[T]]): Option[C[T]] = {
       val b = cbf.newBuilder
-      for (t <- ts)
+      for (t <- ts.iterator)
         if (t.isEmpty)
           return None
         else
@@ -101,9 +88,7 @@ package utils {
   }
 }
 
-package object utils
-    extends richUtils.Implicits with NumericPairImplicits with utils.NumericImplicits with Py4jUtils
-    with ErrorHandling {
+package object utils extends ErrorHandling with Logging {
 
   type UtilsType = this.type
 
@@ -120,51 +105,6 @@ package object utils
     l.toInt
   }
 
-  def checkGzipOfGlobbedFiles(
-    globPaths: Seq[String],
-    fileListEntries: Array[FileListEntry],
-    forceGZ: Boolean,
-    gzAsBGZ: Boolean,
-    maxSizeMB: Int = 128,
-  ) = {
-    if (fileListEntries.isEmpty)
-      fatal(s"arguments refer to no files: ${globPaths.toIndexedSeq}.")
-    if (!gzAsBGZ) {
-      fileListEntries.foreach { fileListEntry =>
-        val path = fileListEntry.getPath
-        if (path.endsWith(".gz"))
-          checkGzippedFile(fileListEntry, forceGZ, false, maxSizeMB)
-      }
-    }
-  }
-
-  def checkGzippedFile(
-    fileListEntry: FileListEntry,
-    forceGZ: Boolean,
-    gzAsBGZ: Boolean,
-    maxSizeMB: Int = 128,
-  ): Unit = {
-    if (!forceGZ && !gzAsBGZ)
-      fatal(
-        s"""Cannot load file '${fileListEntry.getPath}'
-           |  .gz cannot be loaded in parallel. Is the file actually *block* gzipped?
-           |  If the file is actually block gzipped (even though its extension is .gz),
-           |  use the 'force_bgz' argument to treat all .gz file extensions as .bgz.
-           |  If you are sure that you want to load a non-block-gzipped file serially
-           |  on one core, use the 'force' argument.""".stripMargin
-      )
-    else if (!gzAsBGZ) {
-      val fileSize = fileListEntry.getLen
-      if (fileSize > 1024 * 1024 * maxSizeMB)
-        logger.warn(
-          s"""file '${fileListEntry.getPath}' is ${readableBytes(fileSize)}
-             |  It will be loaded serially (on one core) due to usage of the 'force' argument.
-             |  If it is actually block-gzipped, either rename to .bgz or use the 'force_bgz'
-             |  argument.""".stripMargin
-        )
-    }
-  }
-
   def plural(n: Int, sing: String): String = plural(n.toLong, sing)
 
   def plural(n: Int, sing: String, plur: String): String = plural(n.toLong, sing, plur)
@@ -275,16 +215,12 @@ package object utils
   }
 
   def someIf[T](p: Boolean, x: => T): Option[T] =
-    if (p)
-      Some(x)
-    else
-      None
+    if (p) Some(x)
+    else None
 
   def nullIfNot(p: Boolean, x: Any): Any =
-    if (p)
-      x
-    else
-      null
+    if (p) x
+    else null
 
   def divOption(num: Double, denom: Double): Option[Double] =
     someIf(denom != 0, num / denom)
@@ -331,35 +267,15 @@ package object utils
   def flushDouble(a: Double): Double =
     if (math.abs(a) < java.lang.Double.MIN_NORMAL) 0.0 else a
 
-  def getPartNumber(fname: String): Int = {
-    val partRegex = """.*/?part-(\d+).*""".r
-
-    fname match {
-      case partRegex(i) => i.toInt
-      case _ => throw new PathIOException(s"invalid partition file '$fname'")
-    }
-  }
-
-  def rowIterator(r: Row): Iterator[Any] = new Iterator[Any] {
-    var idx: Int = 0
-    def hasNext: Boolean = idx < r.size
-
-    def next(): Any = {
-      val a = r(idx)
-      idx += 1
-      a
-    }
-  }
-
   def prettyIdentifier(str: String): String =
-    if (str.matches("""[_a-zA-Z]\w*"""))
-      str
-    else
-      s"`${StringEscapeUtils.escapeString(str, backticked = true)}`"
+    if (str.matches("""[_a-zA-Z]\w*""")) str
+    else s"`${StringEscapeUtils.escapeString(str, backticked = true)}`"
 
-  def formatDouble(d: Double, precision: Int): String = s"%.${precision}f".format(d)
+  def formatDouble(d: Double, precision: Int): String =
+    s"%.${precision}f".format(d)
 
-  def uriPath(uri: String): String = new URI(uri).getPath
+  def uriPath(uri: String): String =
+    new URI(uri).getPath
 
   // NB: can't use Nothing here because it is not a super type of Null
   private object flattenOrNullInstance extends FlattenOrNull[Array]
@@ -414,32 +330,9 @@ package object utils
     m.invoke(obj, args: _*)
   }
 
-  /* Use reflection to get the path of a partition coming from a Parquet read. This requires
-   * accessing Spark internal interfaces. It works with Spark 1 and 2 and doesn't depend on the
-   * location of the Parquet package (parquet vs org.apache.parquet) which can vary between
-   * distributions. */
-  def partitionPath(p: Partition): String = {
-    p.getClass.getCanonicalName match {
-      case "org.apache.spark.rdd.SqlNewHadoopPartition" =>
-        val split = invokeMethod(invokeMethod(p, "serializableHadoopSplit"), "value").asInstanceOf[
-          NewFileSplit
-        ]
-        split.getPath.getName
-
-      case "org.apache.spark.sql.execution.datasources.FilePartition" =>
-        val files = invokeMethod(p, "files").asInstanceOf[Seq[_ <: AnyRef]]
-        assert(files.length == 1)
-        invokeMethod(files(0), "filePath").asInstanceOf[String]
-
-      case "org.apache.spark.rdd.HadoopPartition" =>
-        val split = invokeMethod(invokeMethod(p, "inputSplit"), "value").asInstanceOf[FileSplit]
-        split.getPath.getName
-    }
-  }
-
   def dictionaryOrdering[T](ords: Ordering[T]*): Ordering[T] = {
     new Ordering[T] {
-      def compare(x: T, y: T): Int = {
+      override def compare(x: T, y: T): Int = {
         var i = 0
         while (i < ords.size) {
           val v = ords(i).compare(x, y)
@@ -452,7 +345,8 @@ package object utils
     }
   }
 
-  val defaultJSONFormats: Formats = Serialization.formats(NoTypeHints) + GenericIndexedSeqSerializer
+//  val DefaultFormats: Formats =
+//    Serialization.formats(NoTypeHints) + GenericIndexedSeqSerializer
 
   def box(i: Int): java.lang.Integer = i
 
@@ -544,31 +438,11 @@ package object utils
 
   def digitsNeeded(i: Int): Int = {
     assert(i >= 0)
-    if (i < 10)
-      1
-    else
-      1 + digitsNeeded(i / 10)
+    i.toString.length
   }
 
-  def partFile(numDigits: Int, i: Int): String = {
-    val is = i.toString
-    assert(is.length <= numDigits)
-    "part-" + StringUtils.leftPad(is, numDigits, "0")
-  }
-
-  def partSuffix(ctx: TaskContext): String = {
-    val rng = new java.security.SecureRandom()
-    val fileUUID = new java.util.UUID(rng.nextLong(), rng.nextLong())
-    s"${ctx.stageId()}-${ctx.partitionId()}-${ctx.attemptNumber()}-$fileUUID"
-  }
-
-  def partFile(d: Int, i: Int, ctx: TaskContext): String = s"${partFile(d, i)}-${partSuffix(ctx)}"
-
-  def lift[T, S](pf: PartialFunction[T, S]): (T) => Option[S] = pf.lift
-
-  def flatLift[T, S](pf: PartialFunction[T, Option[S]]): (T) => Option[S] = pf.flatLift
-
-  def optMatch[T, S](a: T)(pf: PartialFunction[T, S]): Option[S] = lift(pf)(a)
+  def lift[T, S](pf: PartialFunction[T, S]): T => Option[S] =
+    pf.lift
 
   def using[R <: AutoCloseable, T](r: R)(consume: (R) => T): T = {
     var caught = false
@@ -669,27 +543,15 @@ package object utils
       s
   }
 
-  def ordMax[T](left: T, right: T, ord: ExtendedOrdering): T =
-    if (ord.gt(left, right))
-      left
-    else
-      right
-
-  def ordMin[T](left: T, right: T, ord: ExtendedOrdering): T =
-    if (ord.lt(left, right))
-      left
-    else
-      right
-
   def makeJavaMap[K, V](x: IterableOnce[(K, V)]): java.util.HashMap[K, V] = {
     val m = new java.util.HashMap[K, V]
-    x.foreach { case (k, v) => m.put(k, v) }
+    x.iterator.foreach { case (k, v) => m.put(k, v) }
     m
   }
 
   def makeJavaSet[K](x: IterableOnce[K]): java.util.HashSet[K] = {
     val m = new java.util.HashSet[K]
-    x.foreach(m.add)
+    x.iterator.foreach(m.add)
     m
   }
 
@@ -698,8 +560,8 @@ package object utils
   )(
     key: T => K,
     value: T => V,
-  ): collection.Map[K, V] = {
-    val it = ts.toIterator
+  ): scala.collection.Map[K, V] = {
+    val it = ts.iterator
     val m = mutable.Map[K, V]()
     while (it.hasNext) {
       val t = it.next()
@@ -739,18 +601,6 @@ package object utils
       dumpClassLoader(parent)
   }
 
-  def writeNativeFileReadMe(fs: FS, path: String): Unit = {
-    val dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss")
-
-    using(new OutputStreamWriter(fs.create(path + "/README.txt"))) { out =>
-      out.write(
-        s"""This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
-           |  Written with version $HAIL_PRETTY_VERSION
-           |  Created at ${dateFormat.format(new Date())}""".stripMargin
-      )
-    }
-  }
-
   def decompress(input: Array[Byte], size: Int): Array[Byte] =
     CompressionUtils.decompressZlib(input, size)
 
@@ -796,18 +646,6 @@ package object utils
     f(s, arg1, arg2, arg3, arg4, arg5, arg6, arg7)
   }
 
-  def drainInputStreamToOutputStream(
-    is: InputStream,
-    os: OutputStream,
-  ): Unit = {
-    val buffer = new Array[Byte](1024)
-    var length = is.read(buffer)
-    while (length != -1) {
-      os.write(buffer, 0, length);
-      length = is.read(buffer)
-    }
-  }
-
   def isJavaIdentifier(id: String): Boolean = {
     if (!java.lang.Character.isJavaIdentifierStart(id.head))
       return false
@@ -949,24 +787,3 @@ package object utils
     unreachable
   }
 }
-
-// FIXME: probably resolved in 3.6 https://github.com/json4s/json4s/commit/fc96a92e1aa3e9e3f97e2e91f94907fdfff6010d
-object GenericIndexedSeqSerializer extends Serializer[IndexedSeq[_]] {
-  val IndexedSeqClass = classOf[IndexedSeq[_]]
-
-  override def serialize(implicit format: Formats) = {
-    case seq: IndexedSeq[_] => JArray(seq.map(Extraction.decompose).toList)
-  }
-
-  override def deserialize(implicit format: Formats) = {
-    case (TypeInfo(IndexedSeqClass, parameterizedType), JArray(xs)) =>
-      val typeInfo = TypeInfo(
-        parameterizedType
-          .map(_.getActualTypeArguments()(0))
-          .getOrElse(throw new RuntimeException("No type parameter info for type IndexedSeq"))
-          .asInstanceOf[Class[_]],
-        None,
-      )
-      xs.map(x => Extraction.extract(x, typeInfo)).toArray[Any]
-  }
-}
diff --git a/hail/hail/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala b/hail/hail/utils/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
similarity index 100%
rename from hail/hail/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
rename to hail/hail/utils/src/is/hail/utils/prettyPrint/PrettyPrintWriter.scala
diff --git a/hail/hail/src/is/hail/utils/prettyPrint/package.scala b/hail/hail/utils/src/is/hail/utils/prettyPrint/package.scala
similarity index 98%
rename from hail/hail/src/is/hail/utils/prettyPrint/package.scala
rename to hail/hail/utils/src/is/hail/utils/prettyPrint/package.scala
index c592341d392..56c23b846e0 100644
--- a/hail/hail/src/is/hail/utils/prettyPrint/package.scala
+++ b/hail/hail/utils/src/is/hail/utils/prettyPrint/package.scala
@@ -1,5 +1,7 @@
 package is.hail.utils
 
+import is.hail.collection.implicits.toRichIterable
+
 package object prettyPrint {
   implicit def text(t: String): Doc = Text(t)
 
diff --git a/hail/mill-build/build.mill b/hail/mill-build/build.mill
index 267cea4f7f8..d890846d080 100644
--- a/hail/mill-build/build.mill
+++ b/hail/mill-build/build.mill
@@ -1,61 +1,88 @@
 package build
 
-import mill.*, scalalib.*
+import mill.T
+import mill.api.{PathRef, Task, TaskCtx}
 import mill.meta.MillBuildRootModule
+import mill.scalalib.Dep
 
-object `package` extends MillBuildRootModule {
-  def mvnDeps = Seq(
-    mvn"com.goyeau::mill-scalafix::0.6.0",
-    mvn"org.typelevel::scalac-options:0.1.8",
-  )
+import millbuild.BuildMode
+import millbuild.MvnCoordinate.*
+
+import scala.collection.immutable.ArraySeq
+
+extension [A, F[+X] <: Iterable[X]] (as: F[A])
+  def quoted: Iterable[String] =
+    as.map(i => s"\"$i\"")
+
+  infix def or[B >: A](alternative: => F[B]): F[B] =
+    if as.nonEmpty then as else alternative
+
+
+object `package` extends MillBuildRootModule:
+
+  private val SupportedScalaVersions =
+    Set("2.12", "2.12.13", "2.13")
+
+  override def mvnDeps: T[Seq[Dep]] =
+    Seq(
+      `mill-scalafix` :::: "0.6.0",
+      `scalac-options` :: "0.1.8",
+    )
+    
+  private def customSources: T[Seq[PathRef]] =
+    Task.Sources("mill-build/src")
+
+  override def sources: T[Seq[PathRef]] =
+    super.sources() ++ customSources()
 
   def generatedSources: T[Seq[PathRef]] = Task {
     os.write(
       Task.dest / "BuildConfig.scala",
-      s"""
-         |package millbuild
-         |object BuildConfig{
-         |  def buildMode = "${buildMode()}"
-         |  def enabledScalaVersions = IndexedSeq(${enabledScalaVersions().map(v => s"\"$v\"").mkString(", ")})
+      s"""package millbuild
+         |
+         |import scala.collection.immutable.*
+         |
+         |object BuildConfig {
+         |  val buildMode =
+         |    BuildMode.${buildMode().getOrElse(BuildMode.Release)}
+         |  val enabledScalaVersions =
+         |    ${(enabledScalaVersions() or SupportedScalaVersions.to(ArraySeq)).quoted}
          |}
       """.stripMargin
     )
     super.generatedSources() ++ Seq(PathRef(Task.dest))
   }
 
-  def configDir: T[PathRef] = Task.Source("config")
-
-  def envScalaVersion: T[Option[String]] = Task.Input {
-    Task.env.get("SCALA_VERSION")
-  }
+  def getConfig(name: String)(implicit ctx: TaskCtx.Env): Seq[String] =
+    ctx.env
+      .get(name map { case '-' => '_'; case c => c.toUpper })
+      .orElse {
+        val path = moduleDir / "config" / name
+        Option.when(os.exists(path))(os.read(path))
+      }
+      .to(ArraySeq)
+      .flatMap(_.split(',').map(_.strip))
 
-  def enabledScalaVersions: T[Seq[String]] = Task {
-    val path = configDir().path / "scala-version"
-    val supportedScalaVersions = IndexedSeq("2.12", "2.12.13", "2.13")
-    envScalaVersion()
-      .orElse(Option.when(os.exists(path))(os.read(path).strip))
-      .map { scalaVersion =>
+  def enabledScalaVersions: T[Seq[String]] =
+    Task.Input {
+      getConfig("scala-version").tapEach { ver =>
         require(
-          supportedScalaVersions.contains(scalaVersion),
-          s"SCALA_VERSION must be set to one of 2.12.13, 2.12, or 2.13; found $scalaVersion"
+          SupportedScalaVersions `contains` ver,
+          s"SCALA_VERSION may be one of ${SupportedScalaVersions.quoted.mkString(",")}; found '$ver'."
         )
-        IndexedSeq(scalaVersion)
-      }.getOrElse(supportedScalaVersions)
-  }
+      }
+    }
 
-  def envBuildMode: T[Option[String]] = Task.Input {
-    Task.env.get("HAIL_BUILD_MODE")
-  }
-
-  def buildMode: T[String] = Task {
-    val path = configDir().path / "hail-build-mode"
-    val raw = envBuildMode().orElse(Option.when(os.exists(path))(os.read(path).strip))
-      .getOrElse("Release")
-    val supportedBuildModes = IndexedSeq("dev", "ci", "release")
-    require(
-      supportedBuildModes.contains(raw.toLowerCase),
-      s"HAIL_BUILD_MODE must be set to one of 'dev', 'ci' or 'release'; found '$raw'"
-    )
-    raw.toLowerCase
-  }
-}
\ No newline at end of file
+  def buildMode: T[Option[BuildMode]] =
+    Task.Input {
+      getConfig("hail-build-mode").headOption.map { raw =>
+        try
+          BuildMode.valueOf(raw)
+        catch {
+          case _: Throwable =>
+            sys.error(
+              s"HAIL_BUILD_MODE must be set to one of ${BuildMode.values.mkString("{", ", ", "}")}; found '$raw'"
+            )
+        }
+      }
+    }
\ No newline at end of file
diff --git a/hail/mill-build/mill-build/build.mill b/hail/mill-build/mill-build/build.mill
new file mode 100644
index 00000000000..988c54d772a
--- /dev/null
+++ b/hail/mill-build/mill-build/build.mill
@@ -0,0 +1,5 @@
+package build
+
+import mill.meta.MillBuildRootModule
+
+object `package` extends MillBuildRootModule
\ No newline at end of file
diff --git a/hail/mill-build/mill-build/src/BuildMode.scala b/hail/mill-build/mill-build/src/BuildMode.scala
new file mode 100644
index 00000000000..6139555414c
--- /dev/null
+++ b/hail/mill-build/mill-build/src/BuildMode.scala
@@ -0,0 +1,6 @@
+package millbuild
+
+import upickle.default.ReadWriter
+
+enum BuildMode derives ReadWriter:
+  case Dev, CI, Release
\ No newline at end of file
diff --git a/hail/mill-build/mill-build/src/MvnCoordinate.scala b/hail/mill-build/mill-build/src/MvnCoordinate.scala
new file mode 100644
index 00000000000..31b83b98c61
--- /dev/null
+++ b/hail/mill-build/mill-build/src/MvnCoordinate.scala
@@ -0,0 +1,410 @@
+package millbuild
+
+import mill.scalalib.*
+
+object MvnCoordinate:
+
+  extension (coordinate: String) {
+    infix def ::(version: String): Dep = mvn"$coordinate:$version"
+    infix def ::::(version: String): Dep = mvn"$coordinate::$version"
+    def mvn: Dep = mvn"$coordinate"
+  }
+
+  implicit def mvnCoordinateToDep: String => Dep =
+    _.mvn
+
+  val `accessors-smart` = "net.minidev:accessors-smart"
+  val `activation` = "javax.activation:activation"
+  val `aircompressor` = "io.airlift:aircompressor"
+  val `algebra` = "org.typelevel::algebra"
+  val `all` = "com.github.fommil.netlib:all"
+  val `annotations` = "org.jetbrains:annotations"
+  val `antlr4-runtime` = "org.antlr:antlr4-runtime"
+  val `antlr-runtime` = "org.antlr:antlr-runtime"
+  val `aopalliance` = "aopalliance:aopalliance"
+  val `aopalliance-repackaged` = "org.glassfish.hk2.external:aopalliance-repackaged"
+  val `apacheds-i18n` = "org.apache.directory.server:apacheds-i18n"
+  val `apacheds-kerberos-codec` = "org.apache.directory.server:apacheds-i18n"
+  val `api-asn1-api` = "org.apache.directory.api:api-asn1-api"
+  val `api-util` = "org.apache.directory.api:api-asn1-api"
+  val `asm` = "org.ow2.asm:asm"
+  val `asm-analysis` = "org.ow2.asm:asm-analysis"
+  val `asm-bom` = "org.ow2.asm:asm-bom"
+  val `asm-util` = "org.ow2.asm:asm-util"
+  val `arpack` = "dev.ludovic.netlib:arpack"
+  val `arpack_combined_all` = "dev.ludovic.netlib:arpack_combined_all"
+  val `arrow-format` = "org.apache.arrow:arrow-format"
+  val `arrow-memory` = "org.apache.arrow:arrow-memory"
+  val `arrow-memory-core` = "org.apache.arrow:arrow-memory-core"
+  val `arrow-memory-netty` = "org.apache.arrow:arrow-memory-netty"
+  val `arrow-memory-netty-buffer-patch` = "org.apache.arrow:arrow-memory-netty-buffer-patch"
+  val `arrow-vector` = "org.apache.arrow:arrow-vector"
+  val `audience-annotations` = "org.apache.yetus:audience-annotations"
+  val `automation` = "dk.bricks.automation:automation"
+  val `avro` = "org.apache.avro:avro"
+  val `avro-ipc` = "org.apache.avro:avro-ipc"
+  val `avro-mapred` = "org.apache.avro:avro-mapred"
+  val `azure-core-http-netty` = "com.azure:azure-core-http-netty"
+  val `azure-identity` = "com.azure:azure-identity"
+  val `azure-storage-blob` = "com.azure:azure-storage-blob"
+  val `bcprov-jdk18on` = "org.bouncycastle:bcprov-jdk18on"
+  val `better-monadic-for` = "com.olegpy::better-monadic-for"
+  val `blas` = "dev.ludovic.netlib:blas"
+  val `bonecp` = "org.jolbox:bonecp"
+  val `breeze` = "org.scalanlp::breeze"
+  val `breeze-macros` = "org.scalanlp::breeze-macros"
+  val `breeze-natives` = "org.scalanlp::breeze-natives"
+  val `cats-kernel` = "org.typelevel::cats-kernel"
+  val `chill` = "org.twitter::chill"
+  val `chill-java` = "org.twitter:chill-java"
+  val `commons-beanutils` = "commons-beanutils:commons-beanutils"
+  val `commons-cli` = "commons-cli:commons-cli"
+  val `commons-codec` = "commons-codec:commons-codec"
+  val `commons-collections` = "org.apache.commons:commons-collections"
+  val `commons-collections4` = "org.apache.commons:commons-collections4"
+  val `commons-compiler` = "org.codehaus.janino:commons-compiler"
+  val `commons-compress` = "org.apache.commons:commons-compress"
+  val `commons-configuration` = "commons-configuration:commons-configuration"
+  val `commons-configuration2` = "org.apache.commons:commons-configuration2"
+  val `commons-crypto` = "org.apache.commons:commons-crypto"
+  val `commons-daemon` = "commons-daemon:commons-daemon"
+  val `commons-dhcp` = "commons-dhcp:commons-dhcp"
+  val `commons-digester` = "commons-digester:commons-digester"
+  val `commons-httpclient` = "commons-httpclient:commons-httpclient"
+  val `commons-io` = "commons-io:commons-io"
+  val `commons-lang` = "commons-lang:commons-lang"
+  val `commons-lang3` = "org.apache.commons:commons-lang3"
+  val `commons-logging` = "commons-logging:commons-logging"
+  val `commons-math3` = "org.apache.commons:commons-math3"
+  val `commons-net` = "commons-net:commons-net"
+  val `commons-pool` = "commons-pool:commons-pool"
+  val `commons-text` = "org.apache.commons:commons-text"
+  val `compress-lzf` = "com.ning:compress-lzf"
+  val `core` = "com.github.fommil.netlib:core"
+  val `curator-client` = "org.apache.curator:curator-client"
+  val `curator-framework` = "org.apache.curator:curator-framework"
+  val `curator-recipes` = "org.apache.curator:curator-recipes"
+  val `datanucleus-api-jdo` = "org.datanucleus:datanucleus-api-jdo"
+  val `datanucleus-core` = "org.datanucleus:datanucleus-core"
+  val `datanucleus-rdbms` = "org.datanucleus:datanucleus-rdbms"
+  val `datasketches-java` = "org.apache.datasketches:datasketches-java"
+  val `datasketches-memory` = "org.apache.datasketches:datasketches-memory"
+  val `derby` = "org.apache.derby:derby"
+  val `dnsjava` = "dnsjava:dnsjava"
+  val `dropwizard-metrics-hadoop-metrics2-reporter` = "com.github.joshelser:dropwizard-metrics-hadoop-metrics2-reporter"
+  val `ehcache` = "org.ehcache:ehcache"
+  val `elasticsearch-spark` = "org.elasticsearch::elasticsearch-spark-30"
+  val `error_prone_annotations` = "com.google.errorprone:error_prone_annotations"
+  val `failureaccess` = "com.google.guava:failureaccess"
+  val `freemarker` = "org.freemarker:freemarker"
+  val `flatbuffers-java` = "com.google.flatbuffers:flatbuffers-java"
+  val `gcs-connector` = "com.google.cloud.bigdataoss:gcs-connector"
+  val `generex` = "com.github.mifmif:generex"
+  val `geronimo-jcache_1.0_spec` = "org.apache.geronimo.specs:geronimo-jcache_1.0_spec"
+  val `gson` = "com.google.code.gson:gson"
+  val `guava` = "com.google.guava:guava"
+  val `guice` = "com.google.inject:guice"
+  val `guice-servlet` = "com.google.inject:guice-servlet"
+  val `google-auth-library-oauth2-http` = "com.google.auth:google-auth-library-oauth2-http"
+  val `google-cloud-storage` = "com.google.cloud:google-cloud-storage"
+  val `hadoop-annotations` = "org.apache.hadoop:hadoop-annotations"
+  val `hadoop-auth` = "org.apache.hadoop:hadoop-auth"
+  val `hadoop-client` = "org.apache.hadoop:hadoop-client"
+  val `hadoop-client-api` = "org.apache.hadoop:hadoop-client-api"
+  val `hadoop-client-runtime` = "org.apache.hadoop:hadoop-client-runtime"
+  val `hadoop-common` = "org.apache.hadoop:hadoop-common"
+  val `hadoop-hdfs` = "org.apache.hadoop:hadoop-hdfs"
+  val `hadoop-hdfs-client` = "org.apache.hadoop:hadoop-hdfs-client"
+  val `hadoop-mapreduce-client-app` = "org.apache.hadoop:hadoop-mapreduce-client-app"
+  val `hadoop-mapreduce-client-common` = "org.apache.hadoop:hadoop-mapreduce-client-common"
+  val `hadoop-mapreduce-client-core` = "org.apache.hadoop:hadoop-mapreduce-client-core"
+  val `hadoop-mapreduce-client-jobclient` = "org.apache.hadoop:hadoop-mapreduce-client-jobclient"
+  val `hadoop-mapreduce-client-shuffle` = "org.apache.hadoop:hadoop-mapreduce-client-shuffle"
+  val `hadoop-shaded-guava` = "org.apache.hadoop.thirdparty:hadoop-shaded-guava"
+  val `hadoop-yarn-api` = "org.apache.hadoop:hadoop-yarn-server-api"
+  val `hadoop-yarn-client` = "org.apache.hadoop:hadoop-yarn-client"
+  val `hadoop-yarn-common` = "org.apache.hadoop:hadoop-yarn-common"
+  val `hadoop-yarn-registry` = "org.apache.hadoop:hadoop-yarn-registry"
+  val `hadoop-yarn-server-common` = "org.apache.hadoop:hadoop-yarn-server-common"
+  val `hadoop-yarn-server-web-proxy` = "org.apache.hadoop:hadoop-yarn-server-web-proxy"
+  val `HikariCP` = "com.zaxxer:HakariCP"
+  val `hive-beeline` = "org.apache.hive:hive-beeline"
+  val `hive-cli` = "org.apache.hive:hive-cli"
+  val `hive-common` = "org.apache.hive:hive-common"
+  val `hive-exec` = "org.apache.hive:hive-exec"
+  val `hive-jdbc` = "org.apache.hive:hive-jdbc"
+  val `hive-llap-common` = "org.apache.hive:hive-llap-common"
+  val `hive-metastore` = "org.apache.hive:hive-metastore"
+  val `hive-serde` = "org.apache.hive:hive-serde"
+  val `hive-service-rpc` = "org.apache.hive:hive-service-rpc"
+  val `hive-shims-0.23` = "org.apache.hive:hive-shims-0.23"
+  val `hive-shims` = "org.apache.hive:hive-shims"
+  val `hive-shims-common` = "org.apache.hive:hive-shims-common"
+  val `hive-shims-scheduler` = "org.apache.hive:hive-shims-scheduler"
+  val `hive-storage-api` = "org.apache.hive:hive-storage-api"
+  val `hive-vector-code-gen` = "org.apache.hive:hive-vector-code-gen"
+  val `hk2-api` = "org.glassfish.hk2:hk2-api"
+  val `hk2-locator` = "org.glassfish.hk2:hk2-locator"
+  val `hk2-utils` = "org.glassfish.hk2:hk2-utils"
+  val `htsjdk` = "com.github.samtools:htsjdk"
+  val `htrace-core4` = "org.apache.htrace:htrace-core4"
+  val `httpclient` = "org.apache.httpcomponents:httpclient"
+  val `httpcore` = "org.apache.httpcomponents:httpcore"
+  val `icu4j` = "icu4j:icu4j"
+  val `istack-commons-runtime` = "com.sun.istack:istack-commons-runtime"
+  val `ivy` = "org.apache.ivy:ivy"
+  val `j2objc-annotations` = "com.google.j2objc:j2objc-annotations"
+  val `jackson-annotations` = "com.fasterxml.jackson.core:jackson-annotations"
+  val `jackson-core` = "com.fasterxml.jackson.core:jackson-core"
+  val `jackson-core-asl` = "org.codehaus.jackson:jackson-core-asl"
+  val `jackson-databind` = "com.fasterxml.jackson.core:jackson-databind"
+  val `jackson-dataformat-yaml` = "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml"
+  val `jackson-datatype-jsr310` = "com.fasterxml.jackson.datatype:jackson-datatype-jsr310"
+  val `jackson-jaxrs` = "com.fasterxml.jackson.jaxrs:jackson-jaxrs"
+  val `jackson-jaxrs-base` = "com.fasterxml.jackson.jaxrs:jackson-jaxrs-base"
+  val `jackson-jaxrs-json-provider` = "com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider"
+  val `jackson-mapper-asl` = "org.codehaus.jackson:jackson-mapper-asl"
+  val `jackson-module-jaxb-annotations` = "com.fasterxml.jackson.module::jackson-module-jaxb-annotations"
+  val `jackson-module-paranamer` = "com.fasterxml.jackson.module::jackson-module-paranamer"
+  val `jackson-module-scala` = "com.fasterxml.jackson.module::jackson-module-scala"
+  val `jackson-xc` = "org.codehaus.jackson:jackson-xc"
+  val `jakarta.activation-api` = "jakarta.activation:jakarta.activation-api"
+  val `jakarta.annotation-api` = "jakarta.annotation:jakarta.annotation-api"
+  val `jakarta.inject` = "jakarta.inject:jakarta.inject"
+  val `jakarta.inject-api` = "jakarta.inject:jakarta.inject-api"
+  val `jakarta.servlet-api` = "jakarta.servlet.jakarta.servlet-api"
+  val `jakarta.validation-api` = "jakarta.validation.jakarta.validation-api"
+  val `jakarta.ws.rs-api` = "jakarta.ws.rs:jakarta.ws.rs-api"
+  val `jakarta.xml.bind-api` = "jakara.xml.bind:jakarta.xml.bind-api"
+  val `janino` = "org.codehaus.janino:janino"
+  val `javassist` = "org.javassist:javassist"
+  val `javax.inject` = "javax.inject:javax.inject"
+  val `javax.jdo` = "org.datanucleus:javax.jdo"
+  val `javax.servlet-api` = "javax.servet:javax.servlet-api"
+  val `javolution` = "org.javolution:javolution"
+  val `jaxb-api` = "javax.xml.bind:jaxb-api"
+  val `jaxb-core` = "org.glassfish.jaxb:jaxb-core"
+  val `jaxb-runtime` = "org.glassfish.jaxb:jaxb-runtime"
+  val `jcl-over-slf4j` = "org.slf4j:jcl-over-slf4j"
+  val `jdistlib` = "net.sourceforge.jdistlib:jdistlib"
+  val `jdo-api` = "javax.jdo:jdo-api"
+  val `jersey-client` = "org.glassfish.jersey.core:jersey-client"
+  val `jersey-common` = "org.glassfish.jersey.core:jersey-common"
+  val `jersey-container-servlet` = "org.glassfish.jersey.containers:jersey-container-servlet"
+  val `jersey-container-servlet-core` = "org.glassfish.jersey.containers:jersey-container-servlet-core"
+  val `jersey-media-jaxb` = "org.glassfish.jersey.media:jersey-media-jaxb"
+  val `jersey-hk2` = "org.glassfish.jersey.inject:jersey-hk2"
+  val `jersey-server` = "org.glassfish.jersey.core:jersey-server"
+  val `jjwt-api` = "io.jsonwebtoken:jjwt-api"
+  val `jjwt-impl` = "io.jsonwebtoken:jjwt-impl"
+  val `jjwt-jackson` = "io.jsonwebtoken:jjwt-jackson"
+  val `jetty` = "org.mortbay.jetty:jetty"
+  val `jetty-sslengine` = "org.mortbay.jetty:jetty-sslengine"
+  val `jetty-util` = "org.mortbay.jetty:jetty-util"
+  val `JLargeArrays` = "pl.edu.icm:JLargeArrays"
+  val `jline` = "jline:jline"
+  val `joda-time` = "joda-time:joda-time"
+  val `jodd-core` = "org.jodd:joda-core"
+  val `jpam` = "net.sf.jpam:jpam"
+  val `jna` = "net.java.dev.jna:jna"
+  val `json` = "org.json:json"
+  val `json4s-ast` = "org.json4s::json4s-ast"
+  val `json4s-core` = "org.json4s::json4s-core"
+  val `json4s-jackson` = "org.json4s::json4s-jackson"
+  val `json4s-scalap` = "org.json4s::json4s-scalap"
+  val `json-smart` = "net.minidev:json-smart"
+  val `jsp-api` = "javax.servlet.api:jsp-api"
+  val `jsr305` = "com.google.code.findbugs:jsr305"
+  val `jta` = "javax.transaction:jta"
+  val `JTransforms` = "com.github.wendykierp:JTransforms"
+  val `jul-to-slf4j` = "org.slf4j:jul-to-slf4j"
+  val `junixsocket-core` = "com.kohlschutter.junixsocket:junixsocket-core"
+  val `kerb-admin` = "org.apache.kerby:kerb-admin"
+  val `kerb-client` = "org.apache.kerby:kerb-client"
+  val `kerb-common` = "org.apache.kerby:kerb-common"
+  val `kerb-core` = "org.apache.kerby:kerb-core"
+  val `kerb-crypto` = "org.apache.kerby:kerb-crypto"
+  val `kerb-identity` = "org.apache.kerby:kerb-identity"
+  val `kerb-server` = "org.apache.kerby:kerb-server"
+  val `kerb-simplekdc` = "org.apache.kerby:kerb-simplekdc"
+  val `kerb-util` = "org.apache.kerby:kerb-util"
+  val `kerb-xdr` = "org.apache.kerby:kerb-xdr"
+  val `kryo-shaded` = "com.esotericsoftware:kryo-shaded"
+  val `kubernetes-client` = "io.fabric8:kubernetes-client"
+  val `kubernetes-client-api` = "io.fabric8:kubernetes-client-api"
+  val `kubernetes-httpclient-okhttp` = "io.fabric8:kubernetes-httpclient-okhttp"
+  val `kubernetes-httpclient-vertex` = "io.fabric8:kubernetes-httpclient-vertex"
+  val `kubernetes-model` = "io.fabric8:kubernetes-model"
+  val `kubernetes-model-adminssionregistration` = "io.fabric8:kubernetes-admissionregistration"
+  val `kubernetes-model-apiextensions` = "io.fabric8:kubernetes-apiextensions"
+  val `kubernetes-model-apps` = "io.fabric8:kubernetes-apps"
+  val `kubernetes-model-autoscaling` = "io.fabric8:kubernetes-autoscaling"
+  val `kubernetes-model-batch` = "io.fabric8:kubernetes-batch"
+  val `kubernetes-model-certificates` = "io.fabric8:kubernetes-certificates"
+  val `kubernetes-model-common` = "io.fabric8:kubernetes-common"
+  val `kubernetes-model-coordination` = "io.fabric8:kubernetes-coordination"
+  val `kubernetes-model-core` = "io.fabric8:kubernetes-core"
+  val `kubernetes-model-discovery` = "io.fabric8:kubernetes-discovery"
+  val `kubernetes-model-events` = "io.fabric8:kubernetes-events"
+  val `kubernetes-model-extensions` = "io.fabric8:kubernetes-extensions"
+  val `kubernetes-model-flowcontrol` = "io.fabric8:kubernetes-flowcontrol"
+  val `kubernetes-model-gatewayapi` = "io.fabric8:kubernetes-gatewayapi"
+  val `kubernetes-model-metrics` = "io.fabric8:kubernetes-metrics"
+  val `kubernetes-model-networking` = "io.fabric8:kubernetes-networking"
+  val `kubernetes-model-node` = "io.fabric8:kubernetes-node"
+  val `kubernetes-model-policy` = "io.fabric8:kubernetes-policy"
+  val `kubernetes-model-rbac` = "io.fabric8:kubernetes-rbac"
+  val `kubernetes-model-resource` = "io.fabric8:kubernetes-resource"
+  val `kubernetes-model-scheduling` = "io.fabric8:kubernetes-scheduling"
+  val `kubernetes-model-settings` = "io.fabric8:kubernetes-settings"
+  val `kubernetes-model-storageclass` = "io.fabric8:kubernetes-storageclass"
+  val `lapack` = "dev.ludovic.netlib:lapack"
+  val `leveldbjni-all` = "org.fusesource.leveldbjni:leveldbjni-all"
+  val `libfb303` = "org.apache.trift:libfb303"
+  val `libraries-bom` = "com.google.cloud:libraries-bom"
+  val `libthrift` = "org.apache.thrift:libthrift"
+  val `listenablefuture` = "com.google.guava:listenablefuture"
+  val `log4j` = "log4j:log4j"
+  val `log4j-1.2-api` = "org.apache.logging.log4j:log4j-1.2-api"
+  val `log4j-api` = "org.apache.logging.log4j:log4j-api"
+  val `log4j-api-scala` = "org.apache.logging.log4j::log4j-api-scala"
+  val `log4j-bom` = "org.apache.logging.log4j:log4j-bom"
+  val `log4j-core` = "org.apache.logging.log4j:log4j-core"
+  val `log4j-layout-template-json` = "org.apache.logging.log4j:log4j-layout-template-json"
+  val `log4j-slf4j2-impl` = "org.apache.logging.log4j::log4j-slf4j2-impl"
+  val `logging-interceptor` = "org.squareup.okhttp:logging-interceptor"
+  val `lz4-java` = "org.lz4:lz4-java"
+  val `machinist` = "org.typelevel::machinist"
+  val `macro-compat` = "org.typelevel::macro-compat"
+  val `mainargs` = "com.lihaoyi::mainargs"
+  val `mesos` = "org.apache.mesos:mesos"
+  val `metrics-core` = "io.dropwizard.metrics:metrics-core"
+  val `metrics-graphite` = "io.dropwizard.metrics:metrics-graphite"
+  val `metrics-jmx` = "io.dropwizard.metrics:metrics-jmx"
+  val `metrics-json` = "io.dropwizard.metrics:metrics-json"
+  val `metrics-jvm` = "io.dropwizard.metrics:metrics-jvm"
+  val `mill-scalafix` = "com.goyeau::mill-scalafix"
+  val `minlog` = "com.esotericsoftware:minlog"
+  val `mockito-scala` = "org.mockito::mockito-scala"
+  val `netty-all` = "io.netty:netty-all"
+  val `netty-buffer` = "io.netty:netty-buffer"
+  val `netty-codec` = "io.netty:netty-codec"
+  val `netty-codec-dns` = "io.netty:netty-codec-dns"
+  val `netty-codec-http2` = "io.netty:netty-codec-http2"
+  val `netty-codec-http` = "io.netty:netty-codec-http"
+  val `netty-codec-socks` = "io.netty:netty-codec-socks"
+  val `netty-common` = "io.netty:netty-common"
+  val `netty-handler` = "io.netty:netty-handler"
+  val `netty-handler-proxy` = "io.netty:netty-handler-proxy"
+  val `netty-resolver` = "io.netty:netty-resolver"
+  val `netty-resolver-dns` = "io.netty:netty-resolver-dns"
+  val `netty-tcnative-boringssl-static` = "io.netty:netty-tcnative-boringssl-static"
+  val `netty-tcnative-classes` = "io.netty:netty-tcnative-classes"
+  val `netty-transport` = "io.netty:netty-transport"
+  val `netty-transport-classes-epoll` = "io.netty:netty-transport-classes-epoll"
+  val `netty-transport-classes-kqueue` = "io.netty:netty-transport-classes-kqueue"
+  val `netty-transport-native-epoll` = "io.netty:netty-transport-native-epoll"
+  val `netty-transport-native-kqueue` = "io.netty:netty-transport-native-kqueue"
+  val `netty-transport-native-unix-common` = "io.netty:netty-transport-native-unix-common"
+  val `nimbus-jose-jwt` = "com.nimbusds:nimbus-jose-jwt"
+  val `objenesis` = "org.objenesis:objenesis"
+  val `okhttp` = "org.squareup.okhttp"
+  val `okio` = "org.squareup.okio"
+  val `opencsv` = "com.opencsv:opencsv"
+  val `orc-core` = "org.apache.orc:orc-core"
+  val `orc-format` = "org.apache.orc:orc-format"
+  val `orc-mapreduce` = "org.apache.orc:orc-mapreduce"
+  val `orc-shims` = "org.apache.orc:orc-shims"
+  val `oro` = "oro:oro"
+  val `os-lib` = "com.lihaoyi::os-lib"
+  val `osgi-resource-locator` = "org.glassfish.hk2:osgi-resource-locator"
+  val `paranamer` = "org.throughtworks.paranamer:paranamer"
+  val `parquet-column` = "org.apache.parquet:parquet-column"
+  val `parquet-common` = "org.apache.parquet:parquet-common"
+  val `parquet-format` = "org.apache.parquet:parquet-format"
+  val `parquet-format-structures` = "org.apache.parquet:parquet-format-structures"
+  val `parquet-encoding` = "org.apache.parquet:parquet-encoding"
+  val `parquet-hadoop` = "org.apache.parquet:parquet-hadoop"
+  val `parquet-jackson` = "org.apache.parquet:parquet-jackson"
+  val `protobuf-java` = "org.google.protobuf:protobuf-java"
+  val `pickle` = "net.razorvine:pickle"
+  val `py4j` = "net.sf.py4j:py4j"
+  val `pyrolite` = "net.razorvine:pyrolite"
+  val `pyspark-bom` = "org.apache.spark::pyspark-bom"
+  val `re2j` = "com.google.re2j:re2j"
+  val `RoaringBitmap` = "org.roaringbitmap:RoaringBitmap"
+  val `rocksdbjni` = "org.rocksdb:rocksdbjni"
+  val `scala-collection-compat` = "org.scala-lang.modules::scala-collection-compat"
+  val `scalac-compat-annotation` = "org.typelevel::scalac-compat-annotation"
+  val `scala-compiler` = "org.scala-lang:scala-compiler"
+  val `scala-library` = "org.scala-lang:scala-library"
+  val `scala-parallel-collections` = "org.scala-lang.modules::scala-parallel-collections"
+  val `scala-parser-combinators` = "org.scala-lang.modules::scala-parser-combinators"
+  val `scala-reflect` = "org.scala-lang:scala-reflect"
+  val `scala-xml` = "org.scala-lang.modules::scala-xml"
+  val `scalac-options` = "org.typelevel::scalac-options"
+  val `scalacheck` = "org.scalacheck::scalacheck"
+  val `scalacheck-1-18` = "org.scalatestplus::scalacheck-1-18"
+  val `scalatest` = "org.scalatest::scalatest"
+  val `scalatest-shouldmatchers` = "org.scalatest::scalatest-shouldmatchers"
+  val `scalafix-forbidden-symbol` = "io.github.tanin47::scalafix-forbidden-symbol"
+  val `shims` = "org.roaringbitmap:shims"
+  val `shapeless` = "com.chuusai::shapeless"
+  val `slf4j-api` = "org.slf4j:slf4j-api"
+  val `slf4j-log4j12` = "org.slf4j:slf4j-log4j12"
+  val `snakeyaml` = "org.yaml:snakeyaml"
+  val `snakeyaml-engine` = "org.yaml:snakeyaml-engine"
+  val `snappy-java` = "org.xerial.snappy:snappy-java"
+  val `sourcecode` = "com.lihaoyi::sourcecode"
+  val `spark-catalyst` = "org.apache.spark::spark-catalyst"
+  val `spark-common-utils` = "org.apache.spark::spark-common-utils"
+  val `spark-core` = "org.apache.spark::spark-core"
+  val `spark-graphx` = "org.apache.spark::spark-graphx"
+  val `spark-hive` = "org.apache.spark::spark-hive"
+  val `spark-hive-thriftserver` = "org.apache.spark::spark-hive-thirftserver"
+  val `spark-kubernetes` = "org.apache.spark::spark-kubernetes"
+  val `spark-kvstore` = "org.apache.spark::spark-kvstore"
+  val `spark-launcher` = "org.apache.spark::spark-launcher"
+  val `spark-mesos` = "org.apache.spark::spark-mesos"
+  val `spark-mllib` = "org.apache.spark::spark-mllib"
+  val `spark-mllib-local` = "org.apache.spark::spark-mllib-local"
+  val `spark-network-common` = "org.apache.spark::spark-network-common"
+  val `spark-network-shuffle` = "org.apache.spark::spark-network-shuffle"
+  val `spark-repl` = "org.apache.spark::spark-repl"
+  val `spark-sketch` = "org.apache.spark::spark-sketch"
+  val `spark-sql` = "org.apache.spark::spark-sql"
+  val `spark-sql-api` = "org.apache.spark::spark-sql-api"
+  val `spark-streaming` = "org.apache.spark::spark-streaming"
+  val `spark-tags` = "org.apache.spark::spark-tags"
+  val `spark-unsafe` = "org.apache.spark::spark-unsafe"
+  val `spark-variant` = "org.apache.spark::spark-variant"
+  val `spark-yarn` = "org.apache.spark::spark-yarn"
+  val `spire` = "org.typelevel::spire"
+  val `spire-macros` = "org.typelevel::spire-macros"
+  val `spire-platform` = "org.typelevel::spire-platform"
+  val `spire-util` = "org.typelevel::spire-util"
+  val `ST4` = "org.antlr:ST4"
+  val `stax2-api` = "org.codehaus.woodstox:stax2-api"
+  val `stax-api` = "javax.xml.stream:stax-api"
+  val `stream` = "org.clearspring.analytics:stream"
+  val `super-csv` = "net.sf.supercsv:super-csv"
+  val `testng-7-10` = "org.scalatestplus::testng-7-10"
+  val `threeten-extra` = "org.threeten:threeten-extra"
+  val `tink` = "org.google.crypto.tink:tink"
+  val `transaction-api` = "javax.transaction:transaction-api"
+  val `univocity-parsers` = "com.univocity:univocity-parsers"
+  val `vertx-auth-common` = "io.vertx:vertex-auth-common"
+  val `vertx-core` = "io.vertx:vertex-core"
+  val `vertx-web-client` = "io.vertx:vertex-web-client"
+  val `vertx-web-common` = "io.vertx:vertex-web-common"
+  val `xbean-asm7-shaded` = "org.apache.xbean:xbean-asm7-shaded"
+  val `xbean-asm9-shaded` = "org.apache.xbean:xbean-asm9-shaded"
+  val `xercesImpl` = "xerces:xercesImpl"
+  val `xml-apis` = "xml-apis:xml-apis"
+  val `xmlenc` = "xmlenc:xmlenc"
+  val `xmlschema-core` = "org.apache.ws.xmlschema:xmlschema-core"
+  val `xz` = "org.tukaani:xz"
+  val `zjsonpatch` = "io.fabric8:zjsonpatch"
+  val `zookeeper` = "org.apache.zookeeper"
+  val `zookeeper-jute` = "org.apache.zookeeper-jute"
+  val `zstd-jni` = "com.github.luben:zstd-jni"
\ No newline at end of file
diff --git a/hail/python/dev/pinned-requirements.txt b/hail/python/dev/pinned-requirements.txt
index 38a44fc4e89..34a377d72c9 100644
--- a/hail/python/dev/pinned-requirements.txt
+++ b/hail/python/dev/pinned-requirements.txt
@@ -4,7 +4,7 @@ aiohappyeyeballs==2.6.1
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   aiohttp-devtools
@@ -16,7 +16,7 @@ aiosignal==1.4.0
     #   aiohttp
 alabaster==0.7.16
     # via sphinx
-anyio==4.11.0
+anyio==4.12.1
     # via
     #   httpx
     #   jupyter-server
@@ -35,7 +35,7 @@ asttokens==2.4.1
     # via
     #   devtools
     #   stack-data
-async-lru==2.0.5
+async-lru==2.1.0
     # via jupyterlab
 async-timeout==5.0.1
     # via
@@ -48,17 +48,17 @@ attrs==25.4.0
     #   curlylint
     #   jsonschema
     #   referencing
-babel==2.17.0
+babel==2.18.0
     # via
     #   jupyterlab-server
     #   sphinx
-beautifulsoup4==4.14.2
+beautifulsoup4==4.14.3
     # via nbconvert
 bleach==6.3.0
     # via nbconvert
 build==1.1.1
     # via -r hail/python/dev/requirements.txt
-certifi==2025.11.12
+certifi==2026.1.4
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   httpcore
@@ -92,7 +92,7 @@ curlylint==0.13.1
     # via -r hail/python/dev/requirements.txt
 cycler==0.12.1
     # via matplotlib
-debugpy==1.8.17
+debugpy==1.8.20
     # via ipykernel
 decorator==4.4.2
     # via
@@ -102,7 +102,7 @@ defusedxml==0.7.1
     # via nbconvert
 devtools==0.12.2
     # via aiohttp-devtools
-dill==0.4.0
+dill==0.4.1
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   pylint
@@ -115,7 +115,7 @@ docutils==0.18.1
     #   sphinx-rtd-theme
 entrypoints==0.4
     # via jupyter-client
-exceptiongroup==1.3.0
+exceptiongroup==1.3.1
     # via
     #   anyio
     #   ipython
@@ -128,9 +128,9 @@ executing==2.2.1
     #   stack-data
 fastjsonschema==2.21.2
     # via nbformat
-filelock==3.20.0
+filelock==3.24.3
     # via virtualenv
-fonttools==4.60.1
+fonttools==4.61.1
     # via matplotlib
 fqdn==1.5.1
     # via jsonschema
@@ -147,7 +147,7 @@ httpcore==1.0.9
     # via httpx
 httpx==0.28.1
     # via jupyterlab
-identify==2.6.15
+identify==2.6.16
     # via pre-commit
 idna==3.11
     # via
@@ -159,7 +159,7 @@ idna==3.11
     #   yarl
 imagesize==1.4.1
     # via sphinx
-importlib-metadata==8.7.0
+importlib-metadata==8.7.1
     # via build
 iniconfig==2.3.0
     # via pytest
@@ -170,7 +170,7 @@ ipykernel==6.29.5
     #   jupyterlab
     #   nbclassic
     #   notebook
-ipython==8.37.0
+ipython==8.38.0
     # via
     #   ipykernel
     #   ipywidgets
@@ -197,11 +197,11 @@ jinja2==3.1.6
     #   nbsphinx
     #   notebook
     #   sphinx
-json5==0.12.1
+json5==0.13.0
     # via jupyterlab-server
 jsonpointer==3.0.0
     # via jsonschema
-jsonschema==4.25.1
+jsonschema==4.26.0
     # via
     #   jupyter-events
     #   jupyterlab-server
@@ -240,9 +240,9 @@ jupyter-server==2.17.0
     #   jupyterlab
     #   jupyterlab-server
     #   notebook-shim
-jupyter-server-terminals==0.5.3
+jupyter-server-terminals==0.5.4
     # via jupyter-server
-jupyterlab==4.5.0
+jupyterlab==4.5.4
     # via jupyter
 jupyterlab-pygments==0.3.0
     # via nbconvert
@@ -259,7 +259,7 @@ markupsafe==3.0.3
     #   -c hail/python/dev/../pinned-requirements.txt
     #   jinja2
     #   nbconvert
-matplotlib==3.10.7
+matplotlib==3.10.8
     # via -r hail/python/dev/requirements.txt
 matplotlib-inline==0.2.1
     # via
@@ -267,18 +267,18 @@ matplotlib-inline==0.2.1
     #   ipython
 mccabe==0.7.0
     # via pylint
-mistune==3.1.4
+mistune==3.2.0
     # via nbconvert
 mock==5.1.0
     # via -r hail/python/dev/requirements.txt
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   aiohttp
     #   yarl
 nbclassic==1.3.3
     # via notebook
-nbclient==0.10.2
+nbclient==0.10.4
     # via nbconvert
 nbconvert==7.13.1
     # via
@@ -294,7 +294,7 @@ nbformat==5.10.4
     #   nbconvert
     #   nbsphinx
     #   notebook
-nbsphinx==0.9.7
+nbsphinx==0.9.8
     # via -r hail/python/dev/requirements.txt
 nest-asyncio==1.6.0
     # via
@@ -303,11 +303,11 @@ nest-asyncio==1.6.0
     #   jupyter-client
     #   nbclassic
     #   notebook
-nodeenv==1.9.1
+nodeenv==1.10.0
     # via
     #   pre-commit
     #   pyright
-nodejs-wheel-binaries==24.11.1
+nodejs-wheel-binaries==24.13.1
     # via pyright
 notebook==6.5.7
     # via
@@ -324,7 +324,7 @@ numpy==2.2.6
     #   matplotlib
 overrides==7.7.0
     # via jupyter-server
-packaging==25.0
+packaging==26.0
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   build
@@ -339,7 +339,7 @@ packaging==25.0
     #   sphinx
 pandocfilters==1.5.1
     # via nbconvert
-parso==0.8.5
+parso==0.8.6
     # via jedi
 parsy==1.1.0
     # via curlylint
@@ -347,12 +347,12 @@ pathspec==0.12.1
     # via curlylint
 pexpect==4.9.0
     # via ipython
-pillow==12.0.0
+pillow==12.1.1
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   -r hail/python/dev/requirements.txt
     #   matplotlib
-platformdirs==4.5.0
+platformdirs==4.9.2
     # via
     #   jupyter-core
     #   pylint
@@ -361,7 +361,7 @@ pluggy==1.6.0
     # via pytest
 pre-commit==3.8.0
     # via -r hail/python/dev/requirements.txt
-prometheus-client==0.23.1
+prometheus-client==0.24.1
     # via
     #   jupyter-server
     #   notebook
@@ -374,7 +374,7 @@ propcache==0.4.1
     #   -c hail/python/dev/../pinned-requirements.txt
     #   aiohttp
     #   yarl
-psutil==7.1.3
+psutil==7.2.2
     # via ipykernel
 ptyprocess==0.7.0
     # via
@@ -384,7 +384,7 @@ pure-eval==0.2.3
     # via stack-data
 py==1.11.0
     # via pytest-forked
-pycparser==2.23
+pycparser==3.0
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   cffi
@@ -399,11 +399,11 @@ pygments==2.19.2
     #   sphinx
 pylint==3.3.9
     # via -r hail/python/dev/requirements.txt
-pyparsing==3.2.5
+pyparsing==3.3.2
     # via matplotlib
 pyproject-hooks==1.2.0
     # via build
-pyright==1.1.407
+pyright==1.1.408
     # via -r hail/python/dev/requirements.txt
 pytest==7.4.4
     # via
@@ -476,29 +476,29 @@ rfc3986-validator==0.1.1
     #   jupyter-events
 rfc3987-syntax==1.1.0
     # via jsonschema
-rpds-py==0.29.0
+rpds-py==0.30.0
     # via
     #   jsonschema
     #   referencing
 ruff==0.11.13
     # via -r hail/python/dev/requirements.txt
-send2trash==1.8.3
+send2trash==2.1.0
     # via
     #   jupyter-server
     #   notebook
-setuptools==80.9.0
-    # via jupyterlab
+setuptools==81.0.0
+    # via
+    #   -c hail/python/dev/../pinned-requirements.txt
+    #   jupyterlab
 six==1.17.0
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   asttokens
     #   python-dateutil
     #   rfc3339-validator
-sniffio==1.3.1
-    # via anyio
 snowballstemmer==3.0.1
     # via sphinx
-soupsieve==2.8
+soupsieve==2.8.3
     # via beautifulsoup4
 sphinx==6.2.1
     # via
@@ -535,19 +535,19 @@ terminado==0.18.1
     #   jupyter-server
     #   jupyter-server-terminals
     #   notebook
-tinycss2==1.5.0
+tinycss2==1.5.1
     # via nbconvert
 toml==0.10.2
     # via curlylint
-tomli==2.3.0
+tomli==2.4.0
     # via
     #   build
     #   jupyterlab
     #   pylint
     #   pytest
-tomlkit==0.13.3
+tomlkit==0.14.0
     # via pylint
-tornado==6.5.2
+tornado==6.5.4
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   ipykernel
@@ -577,17 +577,17 @@ types-chardet==5.0.4.6
     # via -r hail/python/dev/requirements.txt
 types-decorator==5.2.0.20251101
     # via -r hail/python/dev/requirements.txt
-types-deprecated==1.3.1.20251101
+types-deprecated==1.3.1.20260130
     # via -r hail/python/dev/requirements.txt
-types-pymysql==1.1.0.20250916
+types-pymysql==1.1.0.20251220
     # via -r hail/python/dev/requirements.txt
-types-python-dateutil==2.9.0.20251115
+types-python-dateutil==2.9.0.20260124
     # via -r hail/python/dev/requirements.txt
 types-pyyaml==6.0.12.20250915
     # via -r hail/python/dev/requirements.txt
 types-requests==2.31.0.6
     # via -r hail/python/dev/requirements.txt
-types-setuptools==80.9.0.20250822
+types-setuptools==82.0.0.20260210
     # via -r hail/python/dev/requirements.txt
 types-six==1.17.0.20251009
     # via -r hail/python/dev/requirements.txt
@@ -612,25 +612,25 @@ typing-extensions==4.15.0
     #   pyright
     #   referencing
     #   virtualenv
-tzdata==2025.2
+tzdata==2025.3
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   arrow
 uri-template==1.3.0
     # via jsonschema
-urllib3==2.5.0
+urllib3==2.6.3
     # via
     #   -c hail/python/dev/../pinned-requirements.txt
     #   requests
-uv==0.9.10
+uv==0.9.30
     # via -r hail/python/dev/requirements.txt
-uv-build==0.9.10
+uv-build==0.9.30
     # via -r hail/python/dev/requirements.txt
-virtualenv==20.35.4
+virtualenv==20.38.0
     # via pre-commit
 watchfiles==1.1.1
     # via aiohttp-devtools
-wcwidth==0.2.14
+wcwidth==0.6.0
     # via prompt-toolkit
 webcolors==25.10.0
     # via jsonschema
diff --git a/hail/python/hail/__init__.py b/hail/python/hail/__init__.py
index c2caa3dc3f8..6cb0e32ee85 100644
--- a/hail/python/hail/__init__.py
+++ b/hail/python/hail/__init__.py
@@ -175,7 +175,6 @@ def version() -> str:
 __all__.extend([x for x in expr.__all__ if not hasattr(builtins, x)])
 del builtins
 
-ir.register_functions()
 ir.register_aggregators()
 
 import warnings
diff --git a/hail/python/hail/backend/backend.py b/hail/python/hail/backend/backend.py
index 7f63f268ac6..868266c8eed 100644
--- a/hail/python/hail/backend/backend.py
+++ b/hail/python/hail/backend/backend.py
@@ -339,9 +339,9 @@ def import_fam(self, path: str, quant_pheno: bool, delimiter: str, missing: str)
         return orjson.loads(fam_json_bytes)
 
     def persist(self, dataset: Dataset) -> Dataset:
-        from hail.context import TemporaryFilename
+        from hail.context import TemporaryDirectory
 
-        tempfile = TemporaryFilename(prefix=f'persist_{type(dataset).__name__}')
+        tempfile = TemporaryDirectory(prefix=f'persist_{type(dataset).__name__}', ensure_exists=False)
         persisted = dataset.checkpoint(tempfile.__enter__())
         self._persisted_locations[persisted] = (tempfile, dataset)
         return persisted
diff --git a/hail/python/hail/backend/local_backend.py b/hail/python/hail/backend/local_backend.py
index 336cbdb35e0..d65f84c2af5 100644
--- a/hail/python/hail/backend/local_backend.py
+++ b/hail/python/hail/backend/local_backend.py
@@ -9,7 +9,7 @@
     raise_when_mismatched_hail_versions,
     start_py4j_gateway,
 )
-from hail.utils.java import scala_object, scala_package_object
+from hail.utils.java import scala_object
 from hail.version import __version__
 from hailtop.aiocloud.aiogoogle import GCSRequesterPaysConfiguration
 
@@ -35,10 +35,10 @@ def create(
             raise_when_mismatched_hail_versions(gateway.jvm)
 
             _is = getattr(gateway.jvm, 'is')
-            py4jutils = scala_package_object(_is.hail.utils)
+            py4jutils = scala_object(_is.hail.utils, 'py4jutils')
             try:
                 if not skip_logging_configuration:
-                    py4jutils.configureLogging(logfile, quiet, append)
+                    py4jutils.pyConfigureLogging(logfile, quiet, append)
 
                 flags = {}
                 if branching_factor is not None:
@@ -54,7 +54,7 @@ def create(
 
                 return backend
             except Py4JJavaError as e:
-                tpl = py4jutils.handleForPython(e.java_exception)
+                tpl = py4jutils.pyHandleException(e.java_exception)
                 deepest, full, error_id = tpl._1(), tpl._2(), tpl._3()
                 raise fatal_error_from_java_error_triplet(deepest, full, error_id) from None
         except:
diff --git a/hail/python/hail/backend/py4j_backend.py b/hail/python/hail/backend/py4j_backend.py
index ba60788a3c3..366f387524a 100644
--- a/hail/python/hail/backend/py4j_backend.py
+++ b/hail/python/hail/backend/py4j_backend.py
@@ -20,7 +20,7 @@
 
 from hail.expr import construct_expr
 from hail.ir import CSERenderer, JavaIR
-from hail.utils.java import Env, FatalError, scala_package_object
+from hail.utils.java import Env, FatalError, scala_object, scala_package_object
 from hail.version import __version__
 from hailtop.aiocloud.aiogoogle import GCSRequesterPaysConfiguration
 from hailtop.aiotools.validators import validate_file
@@ -82,7 +82,7 @@ def raise_when_mismatched_hail_versions(jvm: JVMView) -> None:
         )
 
     _is = getattr(jvm, 'is')
-    jar_version = scala_package_object(_is.hail).HAIL_PRETTY_VERSION()
+    jar_version = scala_package_object(_is.hail).PrettyVersion()
     if jar_version != __version__:
         raise RuntimeError(
             f"Hail version mismatch between JAR and Python library\n  JAR:    {jar_version}\n  Python: {__version__}"
@@ -124,7 +124,7 @@ def deco(*args, **kwargs):
             if not Env.is_fully_initialized():
                 raise ValueError('Error occurred during Hail initialization.') from e
 
-            tpl = Env.jutils().handleForPython(e.java_exception)
+            tpl = Env.jutils().pyHandleException(e.java_exception)
             deepest, full, error_id = tpl._1(), tpl._2(), tpl._3()
             raise fatal_error_from_java_error_triplet(deepest, full, error_id) from None
         except pyspark.sql.utils.CapturedException as e:
@@ -193,8 +193,8 @@ def __init__(
 
         self._jvm = jvm
         self._is = getattr(jvm, 'is')
-        self._utils_package_object = scala_package_object(self._is.hail.utils)
-        self._logger = Log4jLogger(self._utils_package_object)
+        self._py4jutils = scala_object(self._is.hail.utils, 'py4jutils')
+        self._logger = Log4jLogger(self._py4jutils)
 
         self._jbackend = self._is.hail.backend.driver.Py4JQueryDriver(jbackend)
         self._fs = None
@@ -213,8 +213,8 @@ def jvm(self) -> JVMView:
     def hail_package(self) -> JavaPackage:
         return self._is.hail
 
-    def utils_package_object(self) -> JavaObject:
-        return self._utils_package_object
+    def py4jutils(self) -> JavaObject:
+        return self._py4jutils
 
     def validate_file(self, uri: str) -> None:
         fs = self.fs
diff --git a/hail/python/hail/backend/spark_backend.py b/hail/python/hail/backend/spark_backend.py
index 755f53c71a3..76ef58aff83 100644
--- a/hail/python/hail/backend/spark_backend.py
+++ b/hail/python/hail/backend/spark_backend.py
@@ -12,7 +12,7 @@
 from hail.ir import BaseIR
 from hail.table import Table
 from hail.utils import copy_log
-from hail.utils.java import scala_package_object
+from hail.utils.java import scala_object
 from hail.version import __version__
 from hailtop.aiocloud.aiogoogle import GCSRequesterPaysConfiguration
 from hailtop.aiotools.validators import validate_file
@@ -115,9 +115,9 @@ def __init__(
 
         _is = getattr(jvm, 'is')
 
-        py4jutils = scala_package_object(_is.hail.utils)
+        py4jutils = scala_object(_is.hail.utils, 'py4jutils')
         if not skip_logging_configuration:
-            py4jutils.configureLogging(log, quiet, append)
+            py4jutils.pyConfigureLogging(log, quiet, append)
 
         JSparkBackend = _is.hail.backend.spark.SparkBackend
         if sc is not None:
@@ -156,7 +156,7 @@ def validate_file(self, uri: str) -> None:
     @property
     def fs(self) -> FS:
         if self._fs is None:
-            self._fs = HadoopFS(self._utils_package_object, self._jbackend.pyFs())
+            self._fs = HadoopFS(self._py4jutils, self._jbackend.pyFs())
         return self._fs
 
     @fs.setter
diff --git a/hail/python/hail/experimental/context.py b/hail/python/hail/experimental/context.py
index bf482b62a7c..17c4cdd1804 100644
--- a/hail/python/hail/experimental/context.py
+++ b/hail/python/hail/experimental/context.py
@@ -6,7 +6,7 @@
 from hail.backend.py4j_backend import raise_when_mismatched_hail_versions, start_py4j_gateway
 from hail.context import HailContext, _get_log
 from hail.context import init as init_
-from hail.utils.java import BackendType, array_of, choose_backend, scala_object, scala_package_object
+from hail.utils.java import BackendType, array_of, choose_backend, scala_object
 from hail.version import __version__
 from hailtop.aiocloud.aiogoogle import GCSRequesterPaysConfiguration
 from hailtop.config import ConfigVariable, configuration_of, get_remote_tmpdir
@@ -64,11 +64,11 @@ def init(
     try:
         raise_when_mismatched_hail_versions(gateway.jvm)
         _is = getattr(gateway.jvm, 'is')
-        py4jutils = scala_package_object(_is.hail.utils)
+        py4jutils = scala_object(_is.hail.utils, 'py4jutils')
 
         try:
             if not skip_logging_configuration:
-                py4jutils.configureLogging(log, quiet, append)
+                py4jutils.pyConfigureLogging(log, quiet, append)
 
             jbackend = __init_batch_backend(
                 gateway=gateway,
@@ -95,7 +95,7 @@ def init(
 
             HailContext.create(log, quiet, append, default_reference, global_seed, backend)
         except Py4JJavaError as e:
-            tpl = py4jutils.handleForPython(e.java_exception)
+            tpl = py4jutils.pyHandleException(e.java_exception)
             deepest, full, error_id = tpl._1(), tpl._2(), tpl._3()
             raise fatal_error_from_java_error_triplet(deepest, full, error_id) from None
     except:
diff --git a/hail/python/hail/expr/__init__.py b/hail/python/hail/expr/__init__.py
index 3f2fd66b4d3..381d2f4b1f3 100644
--- a/hail/python/hail/expr/__init__.py
+++ b/hail/python/hail/expr/__init__.py
@@ -282,7 +282,6 @@
     tstream,
     tstruct,
     ttuple,
-    tunion,
     tvariable,
     tvoid,
     types_match,
@@ -558,7 +557,6 @@
     'tstruct',
     'ttable',
     'ttuple',
-    'tunion',
     'tuple',
     'tvariable',
     'tvoid',
diff --git a/hail/python/hail/expr/expressions/expression_typecheck.py b/hail/python/hail/expr/expressions/expression_typecheck.py
index 5c6f5679795..f81554a5b2d 100644
--- a/hail/python/hail/expr/expressions/expression_typecheck.py
+++ b/hail/python/hail/expr/expressions/expression_typecheck.py
@@ -21,7 +21,6 @@
     tstream,
     tstruct,
     ttuple,
-    tunion,
 )
 from hail.typecheck import TypeChecker, TypecheckFailure
 from hail.utils.java import escape_parsable
@@ -443,45 +442,6 @@ def _coerce(self, x: Expression):
         return hl.struct(**{name: c.coerce(x[name]) for name, c in self.fields.items()})
 
 
-class UnionCoercer(ExprCoercer):
-    def __init__(self, cases: Optional[Dict[str, ExprCoercer]] = None):
-        super(UnionCoercer, self).__init__()
-        self.cases = cases
-
-    @property
-    def str_t(self) -> str:
-        if self.cases is None:
-            return 'union'
-        else:
-            case_strs = ', '.join(f'{escape_parsable(name)}: {c.str_t}' for name, c in self.cases.items())
-            return f'union{{{case_strs}}})'
-
-    def _requires_conversion(self, t: HailType) -> bool:
-        assert isinstance(t, tunion)
-        if self.cases is None:
-            return False
-        else:
-            return any(c._requires_conversion(t[name]) for name, c in self.cases.items())
-
-    def can_coerce(self, t: HailType):
-        if self.cases is None:
-            return isinstance(t, tunion)
-        else:
-            return (
-                isinstance(t, tunion)
-                and len(t) == len(self.cases)
-                and all(
-                    expected[0] == actual[0] and expected[1].can_coerce(actual[1])
-                    for expected, actual in zip(self.cases.items(), t.items())
-                )
-            )
-
-    def _coerce(self, x: Expression):
-        assert isinstance(x, hl.expr.StructExpression)
-        assert list(x.keys()) == list(self.cases.keys())
-        raise NotImplementedError()
-
-
 class OneOfExprCoercer(ExprCoercer):
     def __init__(self, *options: ExprCoercer):
         super(OneOfExprCoercer, self).__init__()
@@ -526,7 +486,6 @@ def _coerce(self, x: Expression) -> Expression:
 expr_dict = DictCoercer
 expr_tuple = TupleCoercer
 expr_struct = StructCoercer
-expr_union = UnionCoercer
 expr_numeric = expr_oneof(expr_int32, expr_int64, expr_float32, expr_float64)
 
 primitives: Dict[HailType, ExprCoercer] = {
@@ -541,8 +500,8 @@ def _coerce(self, x: Expression) -> Expression:
 
 
 def coercer_from_dtype(t: HailType) -> ExprCoercer:
-    if t in primitives:
-        return primitives[t]
+    if (c := primitives.get(t)) is not None:
+        return c
     elif isinstance(t, tlocus):
         return expr_locus(t.reference_genome)
     elif isinstance(t, tinterval):
@@ -562,5 +521,4 @@ def coercer_from_dtype(t: HailType) -> ExprCoercer:
     elif isinstance(t, tstruct):
         return expr_struct({name: coercer_from_dtype(t_) for name, t_ in t.items()})
     else:
-        assert isinstance(t, tunion)
-        return expr_union({name: coercer_from_dtype(t_) for name, t_ in t.items()})
+        assert False, f'Unknown dtype: {t}'
diff --git a/hail/python/hail/expr/functions.py b/hail/python/hail/expr/functions.py
index 3eb517f938e..698a0fee7d3 100644
--- a/hail/python/hail/expr/functions.py
+++ b/hail/python/hail/expr/functions.py
@@ -131,8 +131,9 @@ def _seeded_func(name, ret_type, seed, *args):
         static_rng_uid = -seed - 1
     indices, aggregations = unify_all(*args)
     rng_state = ir.Ref('__rng_state', trngstate)
+    rng_state = ir.RNGSplitStatic(rng_state, static_rng_uid)
     return construct_expr(
-        ir.ApplySeeded(name, static_rng_uid, rng_state, ret_type, *(a._ir for a in args)),
+        ir.Apply(name, ret_type, rng_state, *(a._ir for a in args)),
         ret_type,
         indices,
         aggregations,
diff --git a/hail/python/hail/expr/type_parsing.py b/hail/python/hail/expr/type_parsing.py
index f3f03b19d67..8d95b70a0cd 100644
--- a/hail/python/hail/expr/type_parsing.py
+++ b/hail/python/hail/expr/type_parsing.py
@@ -6,7 +6,7 @@
 from . import types
 
 type_grammar_str = r"""
-    type = _ ( array / bool / call / dict / interval / int64 / int32 / float32 / float64 / locus / ndarray / rng_state / set / stream / struct / str / tuple / union / void / variable ) _
+    type = _ ( array / bool / call / dict / interval / int64 / int32 / float32 / float64 / locus / ndarray / rng_state / set / stream / struct / str / tuple / void / variable ) _
     variable = "?" simple_identifier (":" simple_identifier)?
     void = "void" / "tvoid"
     int64 = "int64" / "tint64"
@@ -23,7 +23,6 @@
     stream = ("tstream" / "stream") _ "<" type ">"
     dict = ("tdict" / "dict") _ "<" type "," type ">"
     struct = ("tstruct" / "struct") _ "{" (fields / _) "}"
-    union = ("tunion" / "union") _ "{" (fields / _) "}"
     tuple = ("ttuple" / "tuple") _ "(" ((type ("," type)*) / _) ")"
     fields = field ("," field)*
     field = identifier ":" type
@@ -112,14 +111,6 @@ def visit_struct(self, node, visited_children):
             fields = maybe_fields[0]
             return types.tstruct(**dict(fields))
 
-    def visit_union(self, node, visited_children):
-        tunion, _, brace, maybe_fields, brace = visited_children  # noqa: PLW0128
-        if not maybe_fields:
-            return types.tunion()
-        else:
-            fields = maybe_fields[0]
-            return types.tunion(**dict(fields))
-
     def visit_tuple(self, node, visited_children):
         ttuple, _, paren, [maybe_types], paren = visited_children  # noqa: PLW0128
         if not maybe_types:
diff --git a/hail/python/hail/expr/types.py b/hail/python/hail/expr/types.py
index 4c053855052..8aa9ffce9f5 100644
--- a/hail/python/hail/expr/types.py
+++ b/hail/python/hail/expr/types.py
@@ -51,7 +51,6 @@
     'tstream',
     'tstruct',
     'ttuple',
-    'tunion',
     'tvariable',
     'tvoid',
     'types_match',
@@ -1505,97 +1504,6 @@ def _get_context(self):
         return HailTypeContext.union(*self.values())
 
 
-class tunion(HailType, Mapping):
-    @typecheck_method(case_types=hail_type)
-    def __init__(self, **case_types):
-        """Tagged union type.  Values of type union represent one of several
-        heterogenous, named cases.
-
-        Parameters
-        ----------
-        cases : keyword args of :class:`.HailType`
-            The union cases.
-
-        """
-
-        super(tunion, self).__init__()
-        self._case_types = case_types
-        self._cases = tuple(case_types)
-
-    @property
-    def cases(self):
-        """Return union case names.
-
-        Returns
-        -------
-        :obj:`tuple` of :class:`str`
-            Tuple of union case names
-        """
-        return self._cases
-
-    @typecheck_method(item=oneof(int, str))
-    def __getitem__(self, item):
-        if isinstance(item, int):
-            item = self._cases[item]
-        return self._case_types[item]
-
-    def __iter__(self):
-        return iter(self._case_types)
-
-    def __len__(self):
-        return len(self._cases)
-
-    def __str__(self):
-        return "union{{{}}}".format(', '.join('{}: {}'.format(escape_parsable(f), str(t)) for f, t in self.items()))
-
-    def _eq(self, other):
-        return (
-            isinstance(other, tunion) and self._cases == other._cases and all(self[c] == other[c] for c in self._cases)
-        )
-
-    def _pretty(self, b, indent, increment):
-        if not self._cases:
-            b.append('union {}')
-            return
-
-        pre_indent = indent
-        indent += increment
-        b.append('union {')
-        for i, (f, t) in enumerate(self.items()):
-            if i > 0:
-                b.append(', ')
-            b.append('\n')
-            b.append(' ' * indent)
-            b.append('{}: '.format(escape_parsable(f)))
-            t._pretty(b, indent, increment)
-        b.append('\n')
-        b.append(' ' * pre_indent)
-        b.append('}')
-
-    def _parsable_string(self):
-        return "Union{{{}}}".format(
-            ','.join('{}:{}'.format(escape_parsable(f), t._parsable_string()) for f, t in self.items())
-        )
-
-    def unify(self, t):
-        if not (isinstance(t, tunion) and len(self) == len(t)):
-            return False
-        for (f1, t1), (f2, t2) in zip(self.items(), t.items()):
-            if not (f1 == f2 and t1.unify(t2)):
-                return False
-        return True
-
-    def subst(self):
-        return tunion(**{f: t.subst() for f, t in self.items()})
-
-    def clear(self):
-        for f, t in self.items():
-            t.clear()
-
-    def _get_context(self):
-        return HailTypeContext.union(*self.values())
-
-
 class ttuple(HailType, Sequence):
     """Hail type for tuples.
 
@@ -2267,7 +2175,7 @@ def is_container(t) -> bool:
 
 @typecheck(t=HailType)
 def is_compound(t) -> bool:
-    return is_container(t) or isinstance(t, (tstruct, tunion, ttuple, tndarray))
+    return is_container(t) or isinstance(t, (tstruct, ttuple, tndarray))
 
 
 def types_match(left, right) -> bool:
@@ -2334,7 +2242,6 @@ class tvariable(HailType):
         'float64': lambda x: x == tfloat64,
         'locus': lambda x: isinstance(x, tlocus),
         'struct': lambda x: isinstance(x, tstruct),
-        'union': lambda x: isinstance(x, tunion),
         'tuple': lambda x: isinstance(x, ttuple),
     }
 
diff --git a/hail/python/hail/fs/hadoop_fs.py b/hail/python/hail/fs/hadoop_fs.py
index b90e8662d07..ba881b9bc76 100644
--- a/hail/python/hail/fs/hadoop_fs.py
+++ b/hail/python/hail/fs/hadoop_fs.py
@@ -36,8 +36,8 @@ def _file_list_entry_scala_to_python(file_list_entry: Dict[str, Any]) -> FileLis
 
 
 class HadoopFS(FS):
-    def __init__(self, utils_package_object, jfs):
-        self._utils_package_object = utils_package_object
+    def __init__(self, py4jutils, jfs):
+        self._py4jutils = py4jutils
         self._jfs = jfs
 
     def open(self, path: str, mode: str = 'r', buffer_size: int = 8192):
@@ -86,17 +86,15 @@ def fast_stat(self, path: str) -> FileStatus:
         does not affect the behaviors of this method.
 
         """
-        file_status_dict = json.loads(self._utils_package_object.fileStatus(self._jfs, path))
+        file_status_dict = json.loads(self._py4jutils.pyFileStatus(self._jfs, path))
         return _file_status_scala_to_python(file_status_dict)
 
     def stat(self, path: str) -> FileListEntry:
-        file_list_entry_dict = json.loads(self._utils_package_object.fileListEntry(self._jfs, path))
+        file_list_entry_dict = json.loads(self._py4jutils.pyFileListEntry(self._jfs, path))
         return _file_list_entry_scala_to_python(file_list_entry_dict)
 
     def ls(self, path: str) -> List[FileListEntry]:
-        return [
-            _file_list_entry_scala_to_python(st) for st in json.loads(self._utils_package_object.ls(self._jfs, path))
-        ]
+        return [_file_list_entry_scala_to_python(st) for st in json.loads(self._py4jutils.pyLs(self._jfs, path))]
 
     def mkdir(self, path: str) -> None:
         return self._jfs.mkDir(path)
@@ -119,9 +117,9 @@ def __init__(self, hfs, path, buffer_size, use_codec=False):
         super(HadoopReader, self).__init__()
         self._seekable = not use_codec
         if use_codec:
-            self._jfile = hfs._utils_package_object.readFileCodec(hfs._jfs, path, buffer_size)
+            self._jfile = hfs._py4jutils.pyReadFileCodec(hfs._jfs, path, buffer_size)
         else:
-            self._jfile = hfs._utils_package_object.readFile(hfs._jfs, path, buffer_size)
+            self._jfile = hfs._py4jutils.pyReadFile(hfs._jfs, path, buffer_size)
         self.mode = 'rb'
 
     def close(self):
@@ -152,9 +150,9 @@ class HadoopWriter(io.RawIOBase):
     def __init__(self, hfs, path, exclusive=False, use_codec=False):
         super(HadoopWriter, self).__init__()
         if use_codec:
-            self._jfile = hfs._utils_package_object.writeFileCodec(hfs._jfs, path, exclusive)
+            self._jfile = hfs._py4jutils.pyWriteFileCodec(hfs._jfs, path, exclusive)
         else:
-            self._jfile = hfs._utils_package_object.writeFile(hfs._jfs, path, exclusive)
+            self._jfile = hfs._py4jutils.pyWriteFile(hfs._jfs, path, exclusive)
         if exclusive:
             self.mode = 'xb'
         else:
diff --git a/hail/python/hail/ir/__init__.py b/hail/python/hail/ir/__init__.py
index 1c4f9f874f3..8a49786cae1 100644
--- a/hail/python/hail/ir/__init__.py
+++ b/hail/python/hail/ir/__init__.py
@@ -54,7 +54,6 @@
     ApplyBinaryPrimOp,
     ApplyComparisonOp,
     ApplyScanOp,
-    ApplySeeded,
     ApplyUnaryPrimOp,
     ArrayLen,
     ArrayMaximalIndependentSet,
@@ -119,6 +118,7 @@
     Recur,
     Ref,
     RNGSplit,
+    RNGSplitStatic,
     RNGStateLiteral,
     SelectedTopLevelReference,
     SelectFields,
@@ -211,7 +211,6 @@
     MatrixWriter,
 )
 from .register_aggregators import register_aggregators
-from .register_functions import register_functions
 from .renderer import (
     CSERenderer,
     ParensRenderer,
@@ -288,7 +287,6 @@
     'ApplyBinaryPrimOp',
     'ApplyComparisonOp',
     'ApplyScanOp',
-    'ApplySeeded',
     'ApplyUnaryPrimOp',
     'ArrayLen',
     'ArrayMaximalIndependentSet',
@@ -437,6 +435,7 @@
     'PlainRenderer',
     'ProjectedTopLevelReference',
     'RNGSplit',
+    'RNGSplitStatic',
     'RNGStateLiteral',
     'RQStack',
     'ReadPartition',
@@ -528,7 +527,6 @@
     'finalize_randomness',
     'make_filter_and_replace',
     'register_aggregators',
-    'register_functions',
     'subst',
     'tensor_shape_to_matrix_shape',
     'toArray',
diff --git a/hail/python/hail/ir/ir.py b/hail/python/hail/ir/ir.py
index cac9455192d..63bba932288 100644
--- a/hail/python/hail/ir/ir.py
+++ b/hail/python/hail/ir/ir.py
@@ -3223,36 +3223,6 @@ def _compute_type(self, env, agg_env, deep_typecheck):
         return self.return_type
 
 
-class ApplySeeded(IR):
-    @typecheck_method(function=str, static_rng_uid=int, rng_state=IR, return_type=hail_type, args=IR)
-    def __init__(self, function, static_rng_uid, rng_state, return_type, *args):
-        super().__init__(rng_state, *args)
-        self.function = function
-        self.args = args
-        self.rng_state = rng_state
-        self.static_rng_uid = static_rng_uid
-        self.return_type = return_type
-
-    def copy(self, rng_state, *args):
-        return ApplySeeded(self.function, self.static_rng_uid, rng_state, self.return_type, *args)
-
-    def head_str(self):
-        return f'{escape_id(self.function)} {self.static_rng_uid} {self.return_type._parsable_string()}'
-
-    def _eq(self, other):
-        return (
-            other.function == self.function
-            and other.static_rng_uid == self.static_rng_uid
-            and other.return_type == self.return_type
-        )
-
-    def _compute_type(self, env, agg_env, deep_typecheck):
-        for arg in self.args:
-            arg.compute_type(env, agg_env, deep_typecheck)
-
-        return self.return_type
-
-
 class RNGStateLiteral(IR):
     @typecheck_method()
     def __init__(self):
@@ -3281,6 +3251,24 @@ def _compute_type(self, env, agg_env, deep_typecheck):
         return trngstate
 
 
+class RNGSplitStatic(IR):
+    @typecheck_method(rng_state=IR, static_uid=int)
+    def __init__(self, rng_state, static_uid):
+        super().__init__(rng_state)
+        self.rng_state = rng_state
+        self.static_uid = static_uid
+
+    def head_str(self):
+        return str(self.static_uid)
+
+    def copy(self, rng_state):
+        return RNGSplitStatic(rng_state, self.static_uid)
+
+    def _compute_type(self, env, agg_env, deep_typecheck):
+        self.rng_state.compute_type(env, agg_env, deep_typecheck)
+        return trngstate
+
+
 class TableCount(IR):
     @typecheck_method(child=TableIR)
     def __init__(self, child):
diff --git a/hail/python/hail/ir/register_functions.py b/hail/python/hail/ir/register_functions.py
deleted file mode 100644
index 12c019b563e..00000000000
--- a/hail/python/hail/ir/register_functions.py
+++ /dev/null
@@ -1,1385 +0,0 @@
-from hail.expr.nat import NatVariable
-from hail.expr.types import dtype, tarray, tfloat32, tfloat64, tint32, tint64, tndarray, tvariable
-
-from .ir import register_function, register_seeded_function
-
-vcf_header_type_str = (
-    "struct{sampleIDs: array<str>, "
-    "infoFields: array<tuple(str, str)>, "
-    "formatFields: array<tuple(str, str)>, "
-    "filterAttrs: dict<str, dict<str, str>>, "
-    "infoAttrs: dict<str, dict<str, str>>, "
-    "formatAttrs: dict<str, dict<str, str>>, "
-    "infoFlagFields: array<str>}"
-)
-
-
-def register_functions():
-    locusVar = tvariable("R", "locus")
-
-    register_function("isValidContig", (dtype("str"),), dtype("bool"), (locusVar,))
-    register_function(
-        "isValidLocus",
-        (
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("bool"),
-        (locusVar,),
-    )
-    register_function("contigLength", (dtype("str"),), dtype("int32"), (locusVar,))
-    register_function(
-        "getReferenceSequenceFromValidLocus",
-        (
-            dtype("str"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-        (locusVar,),
-    )
-    register_function(
-        "getReferenceSequence",
-        (
-            dtype("str"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-        (locusVar,),
-    )
-
-    register_function("parse_json", (dtype("str"),), dtype("tuple(?T)"), (dtype("?T"),))
-
-    register_function("flatten", (dtype("array<array<?T>>"),), dtype("array<?T>"))
-    register_function(
-        "difference",
-        (
-            dtype("set<?T>"),
-            dtype("set<?T>"),
-        ),
-        dtype("set<?T>"),
-    )
-    register_function("median", (dtype("set<?T:numeric>"),), dtype("?T"))
-    register_function("median", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function("uniqueMinIndex", (dtype("array<?T>"),), dtype("int32"))
-    register_function("mean", (dtype("array<?T:numeric>"),), dtype("float64"))
-    register_function("toFloat32", (dtype("?T:numeric"),), dtype("float32"))
-    register_function("uniqueMaxIndex", (dtype("array<?T>"),), dtype("int32"))
-    register_function("toSet", (dtype("array<?T>"),), dtype("set<?T>"))
-
-    def array_floating_point_divide(arg_type, ret_type):
-        register_function(
-            "div",
-            (
-                arg_type,
-                tarray(arg_type),
-            ),
-            tarray(ret_type),
-        )
-        register_function("div", (tarray(arg_type), arg_type), tarray(ret_type))
-        register_function("div", (tarray(arg_type), tarray(arg_type)), tarray(ret_type))
-
-    array_floating_point_divide(tint32, tfloat32)
-    array_floating_point_divide(tint64, tfloat32)
-    array_floating_point_divide(tfloat32, tfloat32)
-    array_floating_point_divide(tfloat64, tfloat64)
-
-    def ndarray_floating_point_divide(arg_type, ret_type):
-        register_function(
-            "div",
-            (
-                arg_type,
-                tndarray(arg_type, NatVariable()),
-            ),
-            tndarray(ret_type, NatVariable()),
-        )
-        register_function("div", (tndarray(arg_type, NatVariable()), arg_type), tndarray(ret_type, NatVariable()))
-        register_function(
-            "div",
-            (tndarray(arg_type, NatVariable()), tndarray(arg_type, NatVariable())),
-            tndarray(ret_type, NatVariable()),
-        )
-
-    ndarray_floating_point_divide(tint32, tfloat32)
-    ndarray_floating_point_divide(tint64, tfloat32)
-    ndarray_floating_point_divide(tfloat32, tfloat32)
-    ndarray_floating_point_divide(tfloat64, tfloat64)
-    register_function("values", (dtype("dict<?key, ?value>"),), dtype("array<?value>"))
-    register_function(
-        "sliceRight",
-        (
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "get",
-        (
-            dtype("dict<?key, ?value>"),
-            dtype("?key"),
-        ),
-        dtype("?value"),
-    )
-    register_function(
-        "get",
-        (
-            dtype("dict<?key, ?value>"),
-            dtype("?key"),
-            dtype("?value"),
-        ),
-        dtype("?value"),
-    )
-    register_function("max", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function("nanmax", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function(
-        "max",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "nanmax",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "max_ignore_missing",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "nanmax_ignore_missing",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function("product", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function("toInt32", (dtype("?T:numeric"),), dtype("int32"))
-    register_function(
-        "extend",
-        (
-            dtype("array<?T>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function("argmin", (dtype("array<?T>"),), dtype("int32"))
-    register_function("toFloat64", (dtype("?T:numeric"),), dtype("float64"))
-    register_function("sort", (dtype("array<?T>"),), dtype("array<?T>"))
-    register_function(
-        "sort",
-        (
-            dtype("array<?T>"),
-            dtype("bool"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "isSubset",
-        (
-            dtype("set<?T>"),
-            dtype("set<?T>"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "slice",
-        (
-            dtype("str"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<float64>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<float64>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<float64>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "append",
-        (
-            dtype("array<?T>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "sliceLeft",
-        (
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "remove",
-        (
-            dtype("set<?T>"),
-            dtype("?T"),
-        ),
-        dtype("set<?T>"),
-    )
-    register_function(
-        "index",
-        (
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-    )
-    register_function("indexArray", (dtype("array<?T>"), dtype("int32"), dtype("str")), dtype("?T"))
-    register_function(
-        "index",
-        (
-            dtype("dict<?key, ?value>"),
-            dtype("?key"),
-        ),
-        dtype("?value"),
-    )
-    register_function("dictToArray", (dtype("dict<?key, ?value>"),), dtype("array<tuple(?key, ?value)>"))
-    register_function(
-        "mod",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function("dict", (dtype("array<tuple(?key, ?value)>"),), dtype("dict<?key, ?value>"))
-    register_function("dict", (dtype("set<tuple(?key, ?value)>"),), dtype("dict<?key, ?value>"))
-    register_function("keys", (dtype("dict<?key, ?value>"),), dtype("array<?key>"))
-    register_function("min", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function("nanmin", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function(
-        "min",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "nanmin",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "min_ignore_missing",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function(
-        "nanmin_ignore_missing",
-        (
-            dtype("?T"),
-            dtype("?T"),
-        ),
-        dtype("?T"),
-    )
-    register_function("sum", (dtype("array<?T:numeric>"),), dtype("?T"))
-    register_function("toInt64", (dtype("?T:numeric"),), dtype("int64"))
-    register_function(
-        "contains",
-        (
-            dtype("dict<?key, ?value>"),
-            dtype("?key"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "contains",
-        (
-            dtype("array<?T>"),
-            dtype("?T"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "contains",
-        (
-            dtype("set<?T>"),
-            dtype("?T"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "-",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function("addone", (dtype("int32"),), dtype("int32"))
-    register_function("isEmpty", (dtype("dict<?key, ?value>"),), dtype("bool"))
-    register_function("isEmpty", (dtype("array<?T>"),), dtype("bool"))
-    register_function("isEmpty", (dtype("set<?T>"),), dtype("bool"))
-    register_function(
-        "union",
-        (
-            dtype("set<?T>"),
-            dtype("set<?T>"),
-        ),
-        dtype("set<?T>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "mul",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "intersection",
-        (
-            dtype("set<?T>"),
-            dtype("set<?T>"),
-        ),
-        dtype("set<?T>"),
-    )
-    register_function(
-        "add",
-        (
-            dtype("set<?T>"),
-            dtype("?T"),
-        ),
-        dtype("set<?T>"),
-    )
-    register_function("argmax", (dtype("array<?T>"),), dtype("int32"))
-    register_function(
-        "floordiv",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "floordiv",
-        (
-            dtype("array<?T:numeric>"),
-            dtype("?T"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "floordiv",
-        (
-            dtype("?T:numeric"),
-            dtype("array<?T>"),
-        ),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "floordiv",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "floordiv",
-        (
-            dtype("ndarray<?T:numeric, ?nat>"),
-            dtype("?T"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function(
-        "floordiv",
-        (
-            dtype("?T:numeric"),
-            dtype("ndarray<?T, ?nat>"),
-        ),
-        dtype("ndarray<?T, ?nat>"),
-    )
-    register_function("keySet", (dtype("dict<?key, ?value>"),), dtype("set<?key>"))
-    register_function("qnorm", (dtype("float64"),), dtype("float64"))
-    register_function(
-        "oneHotAlleles",
-        (
-            dtype("call"),
-            dtype("int32"),
-        ),
-        dtype("array<int32>"),
-    )
-    register_function(
-        "dpois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "dpois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("ploidy", (dtype("call"),), dtype("int32"))
-    register_function(
-        "lor",
-        (
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "ppois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "ppois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("log10", (dtype("float64"),), dtype("float64"))
-    register_function("isHet", (dtype("call"),), dtype("bool"))
-    register_function("add_on_contig", (dtype("?T:locus"), dtype("int32")), dtype("?T:locus"))
-    register_function("contig_idx", (dtype("?T:locus")), dtype("int32"))
-    register_function("isAutosomalOrPseudoAutosomal", (dtype("?T:locus"),), dtype("bool"))
-    register_function(
-        "testCodeUnification",
-        (
-            dtype("?x:numeric"),
-            dtype("?x:int32"),
-        ),
-        dtype("?x"),
-    )
-    register_seeded_function("rand_pois", (dtype("float64"),), dtype("float64"))
-    register_seeded_function(
-        "rand_pois",
-        (
-            dtype("int32"),
-            dtype("float64"),
-        ),
-        dtype("array<float64>"),
-    )
-    register_function("toFloat32", (dtype("str"),), dtype("float32"))
-    register_function("toFloat32", (dtype("bool"),), dtype("float32"))
-    register_function("isAutosomal", (dtype("?T:locus"),), dtype("bool"))
-    register_function("isPhased", (dtype("call"),), dtype("bool"))
-    register_function("isHomVar", (dtype("call"),), dtype("bool"))
-    register_function(
-        "corr",
-        (
-            dtype("array<float64>"),
-            dtype("array<float64>"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "log",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("log", (dtype("float64"),), dtype("float64"))
-    register_function("foobar2", (), dtype("int32"))
-    register_function(
-        "approxEqual",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("bool"),
-    )
-    register_function("includesEnd", (dtype("interval<?T>"),), dtype("bool"))
-    register_function("position", (dtype("?T:locus"),), dtype("int32"))
-    register_seeded_function(
-        "rand_unif",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_seeded_function("rand_int32", (dtype("int32")), dtype("int32"))
-    register_seeded_function("rand_int64", (dtype("int64"),), dtype("int64"))
-    register_function("showStr", (dtype("?T"), dtype("int32")), dtype("str"))
-    register_function("str", (dtype("?T"),), dtype("str"))
-    register_function(
-        "valuesSimilar",
-        (
-            dtype("?T"),
-            dtype("?T"),
-            dtype('float64'),
-            dtype('bool'),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "replace",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("str"),
-    )
-    register_function("exp", (dtype("float64"),), dtype("float64"))
-    register_function(
-        "land",
-        (
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "compare",
-        (
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("int32"),
-    )
-    register_function("triangle", (dtype("int32"),), dtype("int32"))
-    register_function(
-        "Interval",
-        (
-            dtype("?T"),
-            dtype("?T"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("interval<?T>"),
-    )
-    register_function("contig", (dtype("?T:locus"),), dtype("str"))
-    register_function("Call", (dtype("bool"),), dtype("call"))
-    register_function("Call", (dtype("str"),), dtype("call"))
-    register_function(
-        "Call",
-        (
-            dtype("int32"),
-            dtype("bool"),
-        ),
-        dtype("call"),
-    )
-    register_function(
-        "Call",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("bool"),
-        ),
-        dtype("call"),
-    )
-    register_function(
-        "Call",
-        (
-            dtype("array<int32>"),
-            dtype("bool"),
-        ),
-        dtype("call"),
-    )
-    register_function(
-        "qchisqtail",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "binomTest",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("float64"),
-            dtype("int32"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "qpois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("int32"),
-    )
-    register_function(
-        "qpois",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("int32"),
-    )
-    register_function(
-        "dgamma",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "pgamma",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "qgamma",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("float64"),
-    )
-    register_function("is_finite", (dtype("float32"),), dtype("bool"))
-    register_function("is_finite", (dtype("float64"),), dtype("bool"))
-    register_function("inYPar", (dtype("?T:locus"),), dtype("bool"))
-    register_function(
-        "contingency_table_test",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("struct{p_value: float64, odds_ratio: float64}"),
-    )
-    register_function("toInt32", (dtype("bool"),), dtype("int32"))
-    register_function("toInt32", (dtype("str"),), dtype("int32"))
-    register_function("foobar1", (), dtype("int32"))
-    register_function("toFloat64", (dtype("str"),), dtype("float64"))
-    register_function("toFloat64", (dtype("bool"),), dtype("float64"))
-    register_function(
-        "dbeta",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("Locus", (dtype("str"),), dtype("?T:locus"))
-    register_function(
-        "Locus",
-        (
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("?T:locus"),
-    )
-    register_function("LocusAlleles", (dtype("str"),), dtype("struct{locus: ?T, alleles: array<str>}"))
-    register_function(
-        "LocusInterval",
-        (
-            dtype("str"),
-            dtype("bool"),
-        ),
-        dtype("interval<?T:locus>"),
-    )
-    register_function(
-        "LocusInterval",
-        (
-            dtype("str"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("bool"),
-            dtype("bool"),
-            dtype("bool"),
-        ),
-        dtype("interval<?T:locus>"),
-    )
-    register_function("globalPosToLocus", (dtype("int64"),), dtype("?T:locus"))
-    register_function("locusToGlobalPos", (dtype("?T:locus"),), dtype("int64"))
-    register_function(
-        "liftoverLocus",
-        (
-            dtype("?T:locus"),
-            dtype('float64'),
-        ),
-        dtype("struct{result:?U:locus,is_negative_strand:bool}"),
-    )
-    register_function(
-        "liftoverLocusInterval",
-        (
-            dtype("interval<?T:locus>"),
-            dtype('float64'),
-        ),
-        dtype("struct{result:interval<?U:locus>,is_negative_strand:bool}"),
-    )
-    register_function(
-        "min_rep",
-        (
-            dtype("?T:locus"),
-            dtype("array<str>"),
-        ),
-        dtype("struct{locus: ?T, alleles: array<str>}"),
-    )
-    register_function(
-        "locus_windows_per_contig",
-        (
-            dtype("array<array<float64>>"),
-            dtype("float64"),
-        ),
-        dtype("tuple(array<int32>, array<int32>)"),
-    )
-    register_function("toBoolean", (dtype("str"),), dtype("bool"))
-    register_seeded_function("rand_bool", (dtype("float64"),), dtype("bool"))
-    register_function(
-        "pchisqtail",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_seeded_function("rand_cat", (dtype("array<float64>"),), dtype("int32"))
-    register_function("inYNonPar", (dtype("?T:locus"),), dtype("bool"))
-    register_function(
-        "concat",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("float32"),
-            dtype("float32"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("int64"),
-            dtype("int64"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "pow",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("length", (dtype("str"),), dtype("int32"))
-    register_function(
-        "slice",
-        (
-            dtype("str"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "split",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("int32"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function(
-        "split",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function(
-        "splitQuotedChar",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("array<str>"),
-            dtype("str"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function(
-        "splitQuotedRegex",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("array<str>"),
-            dtype("str"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function(
-        "splitChar",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("array<str>"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function(
-        "splitRegex",
-        (
-            dtype("str"),
-            dtype("str"),
-            dtype("array<str>"),
-        ),
-        dtype("array<str>"),
-    )
-    register_seeded_function(
-        "rand_gamma",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("UnphasedDiploidGtIndexCall", (dtype("int32"),), dtype("call"))
-    register_function(
-        "lgt_to_gt",
-        (
-            dtype("call"),
-            dtype("array<int32>"),
-        ),
-        dtype("call"),
-    )
-    register_function(
-        "local_to_global_g",
-        (dtype("array<?T>"), dtype("array<int32>"), dtype("int32"), dtype("?T")),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "local_to_global_a_r",
-        (dtype("array<?T>"), dtype("array<int32>"), dtype("int32"), dtype("?T"), dtype("bool")),
-        dtype("array<?T>"),
-    )
-    register_function(
-        "index",
-        (
-            dtype("call"),
-            dtype("int32"),
-        ),
-        dtype("int32"),
-    )
-    register_function("sign", (dtype("int64"),), dtype("int64"))
-    register_function("sign", (dtype("float64"),), dtype("float64"))
-    register_function("sign", (dtype("float32"),), dtype("float32"))
-    register_function("sign", (dtype("int32"),), dtype("int32"))
-    register_function("unphasedDiploidGtIndex", (dtype("call"),), dtype("int32"))
-    register_function("gamma", (dtype("float64"),), dtype("float64"))
-    register_function(
-        "mod",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("int64"),
-            dtype("int64"),
-        ),
-        dtype("int64"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("float32"),
-            dtype("float32"),
-        ),
-        dtype("float32"),
-    )
-    register_function(
-        "mod",
-        (
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("int32"),
-    )
-    register_function(
-        "fisher_exact_test",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("struct{p_value: float64, odds_ratio: float64, ci_95_lower: float64, ci_95_upper: float64}"),
-    )
-    register_function("floor", (dtype("float64"),), dtype("float64"))
-    register_function("floor", (dtype("float32"),), dtype("float32"))
-    register_function("isNonRef", (dtype("call"),), dtype("bool"))
-    register_function("includesStart", (dtype("interval<?T>"),), dtype("bool"))
-    register_function("isHetNonRef", (dtype("call"),), dtype("bool"))
-    register_function(
-        "hardy_weinberg_test",
-        (dtype("int32"), dtype("int32"), dtype("int32"), dtype("bool")),
-        dtype("struct{het_freq_hwe: float64, p_value: float64}"),
-    )
-    register_function("haplotype_freq_em", (dtype("array<int32>"),), dtype("array<float64>"))
-    register_function("nNonRefAlleles", (dtype("call"),), dtype("int32"))
-    register_function("abs", (dtype("float64"),), dtype("float64"))
-    register_function("abs", (dtype("float32"),), dtype("float32"))
-    register_function("abs", (dtype("int64"),), dtype("int64"))
-    register_function("abs", (dtype("int32"),), dtype("int32"))
-    register_function(
-        "endswith",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("bool"),
-    )
-    register_function("sqrt", (dtype("float64"),), dtype("float64"))
-    register_function("isnan", (dtype("float32"),), dtype("bool"))
-    register_function("isnan", (dtype("float64"),), dtype("bool"))
-    register_function("lower", (dtype("str"),), dtype("str"))
-    register_seeded_function(
-        "rand_beta",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_seeded_function(
-        "rand_beta",
-        (
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("toInt64", (dtype("bool"),), dtype("int64"))
-    register_function("toInt64", (dtype("str"),), dtype("int64"))
-    register_function("testCodeUnification2", (dtype("?x"),), dtype("?x"))
-    register_function(
-        "contains",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "contains",
-        (
-            dtype("interval<?T>"),
-            dtype("?T"),
-        ),
-        dtype("bool"),
-    )
-    register_function("entropy", (dtype("str"),), dtype("float64"))
-    register_function(
-        "filtering_allele_frequency",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function("gqFromPL", (dtype("array<?N:int32>"),), dtype("int32"))
-    register_function(
-        "startswith",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("bool"),
-    )
-    register_function("ceil", (dtype("float32"),), dtype("float32"))
-    register_function("ceil", (dtype("float64"),), dtype("float64"))
-    register_function("json", (dtype("?T"),), dtype("str"))
-    register_function("strip", (dtype("str"),), dtype("str"))
-    register_function(
-        "firstMatchIn",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("array<str>"),
-    )
-    register_function("isEmpty", (dtype("interval<?T>"),), dtype("bool"))
-    register_function(
-        "~",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "mkString",
-        (
-            dtype("set<str>"),
-            dtype("str"),
-        ),
-        dtype("str"),
-    )
-    register_function(
-        "mkString",
-        (
-            dtype("array<str>"),
-            dtype("str"),
-        ),
-        dtype("str"),
-    )
-    register_function("dosage", (dtype("array<?N:float64>"),), dtype("float64"))
-    register_function("upper", (dtype("str"),), dtype("str"))
-    register_function(
-        "overlaps",
-        (
-            dtype("interval<?T>"),
-            dtype("interval<?T>"),
-        ),
-        dtype("bool"),
-    )
-    register_function(
-        "downcode",
-        (
-            dtype("call"),
-            dtype("int32"),
-        ),
-        dtype("call"),
-    )
-    register_function("inXPar", (dtype("?T:locus"),), dtype("bool"))
-    register_function(
-        "format",
-        (
-            dtype("str"),
-            dtype("?T:tuple"),
-        ),
-        dtype("str"),
-    )
-    register_function("pnorm", (dtype("float64"),), dtype("float64"))
-    register_function("is_infinite", (dtype("float32"),), dtype("bool"))
-    register_function("is_infinite", (dtype("float64"),), dtype("bool"))
-    register_function("isHetRef", (dtype("call"),), dtype("bool"))
-    register_function("isMitochondrial", (dtype("?T:locus"),), dtype("bool"))
-    register_function(
-        "hamming",
-        (
-            dtype("str"),
-            dtype("str"),
-        ),
-        dtype("int32"),
-    )
-    register_function("end", (dtype("interval<?T>"),), dtype("?T"))
-    register_function("start", (dtype("interval<?T>"),), dtype("?T"))
-    register_function("inXNonPar", (dtype("?T:locus"),), dtype("bool"))
-    register_function("escapeString", (dtype("str"),), dtype("str"))
-    register_function("isHomRef", (dtype("call"),), dtype("bool"))
-    register_seeded_function(
-        "rand_norm",
-        (
-            dtype("float64"),
-            dtype("float64"),
-        ),
-        dtype("float64"),
-    )
-    register_function(
-        "chi_squared_test",
-        (
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-            dtype("int32"),
-        ),
-        dtype("struct{p_value: float64, odds_ratio: float64}"),
-    )
-    register_function("strftime", (dtype("str"), dtype("int64"), dtype("str")), dtype("str"))
-    register_function("strptime", (dtype("str"), dtype("str"), dtype("str")), dtype("int64"))
-    register_function(
-        "index_bgen",
-        (dtype("str"), dtype("str"), dtype("dict<str, str>"), dtype('bool'), dtype("int32")),
-        dtype("int64"),
-        (dtype("?T"),),
-    )
-    register_function(
-        "getVCFHeader",
-        (dtype("str"), dtype("str"), dtype("str"), dtype("str")),
-        dtype(vcf_header_type_str),
-    )
diff --git a/hail/python/hail/linalg/blockmatrix.py b/hail/python/hail/linalg/blockmatrix.py
index 175e3dadff5..ea6d755c38a 100644
--- a/hail/python/hail/linalg/blockmatrix.py
+++ b/hail/python/hail/linalg/blockmatrix.py
@@ -66,7 +66,7 @@
     typecheck,
     typecheck_method,
 )
-from hail.utils import local_path_uri, new_local_temp_file, new_temp_file, storage_level, with_local_temp_file
+from hail.utils import local_path_uri, new_local_temp_file, new_temp_file, with_local_temp_file
 from hail.utils.java import Env
 
 block_matrix_type = lazy()
@@ -1328,7 +1328,6 @@ def cache(self):
         """
         return self.persist('MEMORY_ONLY')
 
-    @typecheck_method(storage_level=storage_level)
     def persist(self, storage_level='MEMORY_AND_DISK'):
         """Persists this block matrix in memory or on disk.
 
@@ -1340,11 +1339,6 @@ def persist(self, storage_level='MEMORY_AND_DISK'):
         pipelines. This method is not a substitution for
         :meth:`.BlockMatrix.write`, which stores a permanent file.
 
-        Most users should use the "MEMORY_AND_DISK" storage level. See the `Spark
-        documentation
-        <http://spark.apache.org/docs/latest/programming-guide.html#rdd-persistence>`__
-        for a more in-depth discussion of persisting data.
-
         Parameters
         ----------
         storage_level : str
@@ -1353,12 +1347,15 @@ def persist(self, storage_level='MEMORY_AND_DISK'):
             MEMORY_ONLY_SER_2, MEMORY_AND_DISK, MEMORY_AND_DISK_2,
             MEMORY_AND_DISK_SER, MEMORY_AND_DISK_SER_2, OFF_HEAP
 
+            This parameter no longer does anything and has been retained for
+            compatibility.
+
         Returns
         -------
         :class:`.BlockMatrix`
             Persisted block matrix.
         """
-        return Env.backend().persist_blockmatrix(self)
+        return Env.backend().persist(self)
 
     def unpersist(self):
         """Unpersists this block matrix from memory/disk.
@@ -1373,7 +1370,7 @@ def unpersist(self):
         :class:`.BlockMatrix`
             Unpersisted block matrix.
         """
-        return Env.backend().unpersist_blockmatrix(self)
+        return Env.backend().unpersist(self)
 
     def __pos__(self):
         return self
@@ -2618,7 +2615,7 @@ def _jarray_from_ndarray(nd):
     with with_local_temp_file() as path:
         uri = local_path_uri(path)
         nd.tofile(path)
-        return Env.hail().utils.richUtils.RichArray.importFromDoubles(
+        return Env.hail().io.ArrayImpex.importFromDoubles(
             Env.spark_backend('_jarray_from_ndarray').fs._jfs, uri, nd.size
         )
 
@@ -2626,14 +2623,14 @@ def _jarray_from_ndarray(nd):
 def _ndarray_from_jarray(ja):
     with with_local_temp_file() as path:
         uri = local_path_uri(path)
-        Env.hail().utils.richUtils.RichArray.exportToDoubles(Env.spark_backend('_ndarray_from_jarray').fs._jfs, uri, ja)
+        Env.hail().io.ArrayImpex.exportToDoubles(Env.spark_backend('_ndarray_from_jarray').fs._jfs, uri, ja)
         return np.fromfile(path)
 
 
 def _breeze_fromfile(uri, n_rows, n_cols):
     _check_entries_size(n_rows, n_cols)
 
-    return Env.hail().utils.richUtils.RichDenseMatrixDouble.importFromDoubles(
+    return Env.hail().linalg.implicits.RichDenseMatrixDouble.importFromDoubles(
         Env.spark_backend('_breeze_fromfile').fs._jfs, uri, n_rows, n_cols, True
     )
 
diff --git a/hail/python/hail/methods/impex.py b/hail/python/hail/methods/impex.py
index 8043e82bcd5..d710f12a6b1 100644
--- a/hail/python/hail/methods/impex.py
+++ b/hail/python/hail/methods/impex.py
@@ -3235,10 +3235,21 @@ def index_bgen(
         info(f"indexed {n} sites in {path} at {idx_path}")
 
 
+vcf_header_type_str = (
+    "struct{"
+    "sampleIDs: array<str>, "
+    "infoFields: array<tuple(str, str)>, "
+    "formatFields: array<tuple(str, str)>, "
+    "filterAttrs: dict<str, dict<str, str>>, "
+    "infoAttrs: dict<str, dict<str, str>>, "
+    "formatAttrs: dict<str, dict<str, str>>, "
+    "infoFlagFields: array<str>"
+    "}"
+)
+
+
 @typecheck(path=expr_str, filter=nullable(expr_str), find=nullable(expr_str), replace=nullable(expr_str))
 def get_vcf_header_info(path, filter=None, find=None, replace=None):
-    from hail.ir.register_functions import vcf_header_type_str
-
     return hl.expr.functions._func(
         "getVCFHeader",
         hl.dtype(vcf_header_type_str),
diff --git a/hail/python/hail/utils/java.py b/hail/python/hail/utils/java.py
index 617f0f961b6..60f65ce6381 100644
--- a/hail/python/hail/utils/java.py
+++ b/hail/python/hail/utils/java.py
@@ -56,7 +56,7 @@ def hail():
 
     @staticmethod
     def jutils():
-        return Env.py4j_backend('Env.jutils').utils_package_object()
+        return Env.py4j_backend('Env.jutils').py4jutils()
 
     @staticmethod
     def hc() -> 'hail.context.HailContext':
@@ -142,7 +142,7 @@ def array_of(gateway: JavaGateway, clazz: JavaClass, *elems):
 
 
 def jindexed_seq(x):
-    return Env.jutils().arrayListToISeq(x)
+    return Env.jutils().pyArrayListToISeq(x)
 
 
 def jindexed_seq_args(x):
@@ -152,7 +152,7 @@ def jindexed_seq_args(x):
 
 def jiterable_to_list(it):
     if it is not None:
-        return list(Env.jutils().iterableToArrayList(it))
+        return list(Env.jutils().pyIterableToArrayList(it))
     else:
         return None
 
diff --git a/hail/python/hailtop/hailctl/dev/cli.py b/hail/python/hailtop/hailctl/dev/cli.py
index 613a4626857..6b365a420ef 100644
--- a/hail/python/hailtop/hailctl/dev/cli.py
+++ b/hail/python/hailtop/hailctl/dev/cli.py
@@ -60,7 +60,7 @@ async def _deploy(branch: str, steps: List[str], excluded_steps: List[str], extr
     extra_config_dict = unpack_key_value_inputs(extra_config)
     async with CIClient(deploy_config) as ci_client:
         batch_id = await ci_client.dev_deploy_branch(branch, steps, excluded_steps, extra_config_dict)
-        url = deploy_config.url('ci', f'/batches/{batch_id}')
+        url = deploy_config.url('batch', f'/batches/{batch_id}')
         print(f'Created deploy batch, see {url}')
         if open:
             webbrowser.open(url)
diff --git a/hail/python/hailtop/pinned-requirements.txt b/hail/python/hailtop/pinned-requirements.txt
index eff22825f68..bcadbba044c 100644
--- a/hail/python/hailtop/pinned-requirements.txt
+++ b/hail/python/hailtop/pinned-requirements.txt
@@ -4,40 +4,40 @@ aiodns==2.0.0
     # via -r hail/python/hailtop/requirements.txt
 aiohappyeyeballs==2.6.1
     # via aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via -r hail/python/hailtop/requirements.txt
 aiosignal==1.4.0
     # via aiohttp
+annotated-doc==0.0.4
+    # via typer
 async-timeout==5.0.1
     # via aiohttp
 attrs==25.4.0
     # via aiohttp
 azure-common==1.1.28
     # via azure-mgmt-storage
-azure-core==1.36.0
+azure-core==1.38.2
     # via
     #   azure-identity
     #   azure-mgmt-core
     #   azure-storage-blob
     #   msrest
-azure-identity==1.25.1
+azure-identity==1.25.2
     # via -r hail/python/hailtop/requirements.txt
 azure-mgmt-core==1.6.0
     # via azure-mgmt-storage
 azure-mgmt-storage==20.1.0
     # via -r hail/python/hailtop/requirements.txt
-azure-storage-blob==12.27.1
+azure-storage-blob==12.28.0
     # via -r hail/python/hailtop/requirements.txt
-boto3==1.41.0
+boto3==1.42.53
     # via -r hail/python/hailtop/requirements.txt
-botocore==1.41.0
+botocore==1.42.53
     # via
     #   -r hail/python/hailtop/requirements.txt
     #   boto3
     #   s3transfer
-cachetools==6.2.2
-    # via google-auth
-certifi==2025.11.12
+certifi==2026.1.4
     # via
     #   msrest
     #   requests
@@ -51,26 +51,27 @@ click==8.3.1
     # via typer
 commonmark==0.9.1
     # via rich
-cryptography==46.0.3
+cryptography==46.0.5
     # via
     #   azure-identity
     #   azure-storage-blob
+    #   google-auth
     #   msal
     #   pyjwt
-dill==0.4.0
+dill==0.4.1
     # via -r hail/python/hailtop/requirements.txt
 frozenlist==1.8.0
     # via
     #   -r hail/python/hailtop/requirements.txt
     #   aiohttp
     #   aiosignal
-google-auth==2.43.0
+google-auth==2.48.0
     # via
     #   -r hail/python/hailtop/requirements.txt
     #   google-auth-oauthlib
 google-auth-oauthlib==0.8.0
     # via -r hail/python/hailtop/requirements.txt
-humanize==4.14.0
+humanize==4.15.0
     # via -r hail/python/hailtop/requirements.txt
 idna==3.11
     # via
@@ -82,7 +83,7 @@ isodate==0.7.2
     #   msrest
 janus==1.0.0
     # via -r hail/python/hailtop/requirements.txt
-jmespath==1.0.1
+jmespath==1.1.0
     # via
     #   boto3
     #   botocore
@@ -96,7 +97,7 @@ msal-extensions==1.3.1
     # via azure-identity
 msrest==0.7.1
     # via azure-mgmt-storage
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   aiohttp
     #   yarl
@@ -104,25 +105,25 @@ nest-asyncio==1.6.0
     # via -r hail/python/hailtop/requirements.txt
 oauthlib==3.3.1
     # via requests-oauthlib
-orjson==3.11.4
+orjson==3.11.7
     # via -r hail/python/hailtop/requirements.txt
 propcache==0.4.1
     # via
     #   aiohttp
     #   yarl
-pyasn1==0.6.1
+pyasn1==0.6.2
     # via
     #   pyasn1-modules
     #   rsa
 pyasn1-modules==0.4.2
     # via google-auth
-pycares==4.11.0
+pycares==5.0.1
     # via aiodns
-pycparser==2.23
+pycparser==3.0
     # via cffi
 pygments==2.19.2
     # via rich
-pyjwt==2.10.1
+pyjwt==2.11.0
     # via msal
 python-dateutil==2.9.0.post0
     # via botocore
@@ -146,8 +147,10 @@ rich==12.6.0
     #   typer
 rsa==4.9.1
     # via google-auth
-s3transfer==0.14.0
+s3transfer==0.16.0
     # via boto3
+setuptools==81.0.0
+    # via -r hail/python/hailtop/requirements.txt
 shellingham==1.5.4
     # via typer
 six==1.17.0
@@ -158,7 +161,7 @@ sortedcontainers==2.4.0
     # via -r hail/python/hailtop/requirements.txt
 tabulate==0.9.0
     # via -r hail/python/hailtop/requirements.txt
-typer==0.20.0
+typer==0.24.0
     # via -r hail/python/hailtop/requirements.txt
 typing-extensions==4.15.0
     # via
@@ -169,8 +172,7 @@ typing-extensions==4.15.0
     #   cryptography
     #   janus
     #   multidict
-    #   typer
-urllib3==2.5.0
+urllib3==2.6.3
     # via
     #   botocore
     #   requests
diff --git a/hail/python/hailtop/requirements.txt b/hail/python/hailtop/requirements.txt
index 7cf5d91b685..87da8980f42 100644
--- a/hail/python/hailtop/requirements.txt
+++ b/hail/python/hailtop/requirements.txt
@@ -17,6 +17,7 @@ rich>=12.6.0,<13
 typer>=0.9.0,<1
 python-json-logger>=2.0.2,<3
 pyyaml>=6.0,<7.0
+setuptools>=80.9.0,<82.0.0 # pinned to avoid breaking the build
 sortedcontainers>=2.4.0,<3
 tabulate>=0.8.9,<1
 uvloop>=0.19.0,<0.22.0; sys_platform!='win32' # non-trivial errors raising to 0.22.0; and exclude windows
diff --git a/hail/python/pinned-requirements.txt b/hail/python/pinned-requirements.txt
index da7ede4479e..0138b701089 100644
--- a/hail/python/pinned-requirements.txt
+++ b/hail/python/pinned-requirements.txt
@@ -8,7 +8,7 @@ aiohappyeyeballs==2.6.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -16,6 +16,10 @@ aiosignal==1.4.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   aiohttp
+annotated-doc==0.0.4
+    # via
+    #   -c hail/python/hailtop/pinned-requirements.txt
+    #   typer
 async-timeout==5.0.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
@@ -30,14 +34,14 @@ azure-common==1.1.28
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   azure-mgmt-storage
-azure-core==1.36.0
+azure-core==1.38.2
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   azure-identity
     #   azure-mgmt-core
     #   azure-storage-blob
     #   msrest
-azure-identity==1.25.1
+azure-identity==1.25.2
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -49,27 +53,23 @@ azure-mgmt-storage==20.1.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
-azure-storage-blob==12.27.1
+azure-storage-blob==12.28.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
 bokeh==3.4.3
     # via -r hail/python/requirements.txt
-boto3==1.41.0
+boto3==1.42.53
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
-botocore==1.41.0
+botocore==1.42.53
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
     #   boto3
     #   s3transfer
-cachetools==6.2.2
-    # via
-    #   -c hail/python/hailtop/pinned-requirements.txt
-    #   google-auth
-certifi==2025.11.12
+certifi==2026.1.4
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   msrest
@@ -93,18 +93,19 @@ commonmark==0.9.1
     #   rich
 contourpy==1.3.2
     # via bokeh
-cryptography==46.0.3
+cryptography==46.0.5
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   azure-identity
     #   azure-storage-blob
+    #   google-auth
     #   msal
     #   pyjwt
 decorator==4.4.2
     # via -r hail/python/requirements.txt
 deprecated==1.2.18
     # via -r hail/python/requirements.txt
-dill==0.4.0
+dill==0.4.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -114,7 +115,7 @@ frozenlist==1.8.0
     #   -r hail/python/hailtop/requirements.txt
     #   aiohttp
     #   aiosignal
-google-auth==2.43.0
+google-auth==2.48.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -123,7 +124,7 @@ google-auth-oauthlib==0.8.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
-humanize==4.14.0
+humanize==4.15.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -143,7 +144,7 @@ janus==1.0.0
     #   -r hail/python/hailtop/requirements.txt
 jinja2==3.1.6
     # via bokeh
-jmespath==1.0.1
+jmespath==1.1.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   boto3
@@ -167,7 +168,7 @@ msrest==0.7.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   azure-mgmt-storage
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   aiohttp
@@ -187,11 +188,11 @@ oauthlib==3.3.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   requests-oauthlib
-orjson==3.11.4
+orjson==3.11.7
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
-packaging==25.0
+packaging==26.0
     # via
     #   bokeh
     #   plotly
@@ -201,7 +202,7 @@ pandas==2.3.3
     #   bokeh
 parsimonious==0.11.0
     # via -r hail/python/requirements.txt
-pillow==12.0.0
+pillow==12.1.1
     # via bokeh
 plotly==5.24.1
     # via -r hail/python/requirements.txt
@@ -212,7 +213,7 @@ propcache==0.4.1
     #   yarl
 py4j==0.10.9.7
     # via pyspark
-pyasn1==0.6.1
+pyasn1==0.6.2
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   pyasn1-modules
@@ -221,11 +222,11 @@ pyasn1-modules==0.4.2
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   google-auth
-pycares==4.11.0
+pycares==5.0.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   aiodns
-pycparser==2.23
+pycparser==3.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   cffi
@@ -233,7 +234,7 @@ pygments==2.19.2
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   rich
-pyjwt==2.10.1
+pyjwt==2.11.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   msal
@@ -257,7 +258,7 @@ pyyaml==6.0.3
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
     #   bokeh
-regex==2025.11.3
+regex==2026.2.19
     # via parsimonious
 requests==2.32.5
     # via
@@ -281,12 +282,16 @@ rsa==4.9.1
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   google-auth
-s3transfer==0.14.0
+s3transfer==0.16.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   boto3
 scipy==1.15.3
     # via -r hail/python/requirements.txt
+setuptools==81.0.0
+    # via
+    #   -c hail/python/hailtop/pinned-requirements.txt
+    #   -r hail/python/hailtop/requirements.txt
 shellingham==1.5.4
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
@@ -304,11 +309,11 @@ tabulate==0.9.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
-tenacity==9.1.2
+tenacity==9.1.4
     # via plotly
-tornado==6.5.2
+tornado==6.5.4
     # via bokeh
-typer==0.20.0
+typer==0.24.0
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   -r hail/python/hailtop/requirements.txt
@@ -322,10 +327,9 @@ typing-extensions==4.15.0
     #   cryptography
     #   janus
     #   multidict
-    #   typer
-tzdata==2025.2
+tzdata==2025.3
     # via pandas
-urllib3==2.5.0
+urllib3==2.6.3
     # via
     #   -c hail/python/hailtop/pinned-requirements.txt
     #   botocore
@@ -336,7 +340,7 @@ uvloop==0.21.0
     #   -r hail/python/hailtop/requirements.txt
 wrapt==1.17.3
     # via deprecated
-xyzservices==2025.10.0
+xyzservices==2025.11.0
     # via bokeh
 yarl==1.22.0
     # via
diff --git a/hail/python/test/hail/expr/test_types.py b/hail/python/test/hail/expr/test_types.py
index 20c0b589b2b..0e62243ffe9 100644
--- a/hail/python/test/hail/expr/test_types.py
+++ b/hail/python/test/hail/expr/test_types.py
@@ -21,7 +21,6 @@
     tstr,
     tstruct,
     ttuple,
-    tunion,
 )
 from hail.utils.java import Env
 
@@ -59,9 +58,6 @@ def types_to_test(self):
             tstruct(a=tfloat64, bb=tint32, c=tbool),
             tstruct(a=tint32, b=tint32),
             tstruct(**{'___': tint32, '_ . _': tint32}),
-            tunion(),
-            tunion(a=tint32, b=tstr),
-            tunion(**{'!@#$%^&({[': tstr}),
             ttuple(tstr, tint32),
             ttuple(tarray(tint32), tstr, tstr, tint32, tbool),
             ttuple(),
@@ -141,8 +137,6 @@ def test_get_context(self):
                     tndarray(tstr, 1),
                     tstruct(),
                     tstruct(x=tint32, y=tint64, z=tarray(tset(tstr))),
-                    tunion(),
-                    tunion(a=tint32, b=tstr),
                     ttuple(tstr, tint32),
                     ttuple(),
                 ],
@@ -157,7 +151,6 @@ def test_get_context(self):
                     tinterval(tl1),
                     tset(tinterval(tl1)),
                     tstruct(a=tint32, b=tint32, c=tarray(tl1)),
-                    tunion(a=tint32, b=tl1),
                     ttuple(tarray(tint32), tl1, tstr, tint32, tbool),
                 ],
                 {"GRCh37"},
diff --git a/hail/python/test/hail/linalg/test_linalg.py b/hail/python/test/hail/linalg/test_linalg.py
index df7fbcb787e..655238152bf 100644
--- a/hail/python/test/hail/linalg/test_linalg.py
+++ b/hail/python/test/hail/linalg/test_linalg.py
@@ -254,6 +254,16 @@ def test_block_matrix_from_file():
         _assert_eq(array, data)
 
 
+def test_block_matrix_persist_unpersist():
+    data = np.random.rand(10, 11)
+    bm = BlockMatrix.from_numpy(data, block_size=5)
+    bm_persist = bm.persist()
+    _assert_eq(data, bm_persist.to_numpy())
+
+    bm_unpersist = bm_persist.unpersist()
+    _assert_eq(data, bm_unpersist.to_numpy())
+
+
 @fails_service_backend()
 @fails_local_backend()
 def test_numpy_round_trip_force_blocking():
diff --git a/hail/python/test/hail/test_ir.py b/hail/python/test/hail/test_ir.py
index cdd7b076190..1e335fc199a 100644
--- a/hail/python/test/hail/test_ir.py
+++ b/hail/python/test/hail/test_ir.py
@@ -113,6 +113,7 @@ def aggregate(x):
         ir.NDArrayMatMul(nd, nd),
         ir.LowerBoundOnOrderedCollection(a, i, False),
         ir.GroupByKey(da),
+        ir.RNGSplitStatic(rngState, -1),
         ir.RNGSplit(rngState, ir.MakeTuple([ir.I64(1), ir.I64(2), ir.I64(3)])),
         ir.StreamMap(st, 'unused', v),
         ir.StreamZip([st, st], ['a', 'b'], ir.TrueIR(), 'ExtendNA'),
@@ -180,7 +181,7 @@ def aggregate(x):
     ]
 
 
-static_len_value_irs = 81
+static_len_value_irs = 82
 
 
 @pytest.fixture(params=range(static_len_value_irs))
diff --git a/hail/python/test/hailtop/hailctl/batch/test_submit.py b/hail/python/test/hailtop/hailctl/batch/test_submit.py
index 23014f95ad9..ad817aa5796 100644
--- a/hail/python/test/hailtop/hailctl/batch/test_submit.py
+++ b/hail/python/test/hailtop/hailctl/batch/test_submit.py
@@ -183,7 +183,8 @@ def test_image_environment_variable(submit, tmp_path, client):
 
     b = get_batch_from_json_output(res, client)
     j = b.get_job(1)
-    assert j.status()['spec']['process']['image'] == 'busybox:latest', str(j.status())
+    # Assert ends with because we might be going via the dockerhubproxy image:
+    assert j.status()['spec']['process']['image'].endswith('busybox:latest'), str(j.status())
 
 
 @pytest.mark.xfail(reason='Executable files are not supported.')
diff --git a/hail/scripts/release.sh b/hail/scripts/release.sh
index 2c21d5baddb..21856537288 100755
--- a/hail/scripts/release.sh
+++ b/hail/scripts/release.sh
@@ -24,7 +24,6 @@ usage: $(basename "$0")
         HAIL_GENETICS_HAILTOP_IMAGE=docker://us-docker.pkg.dev/hail-vdc/hail/hailgenetics/hailtop:deploy-123abc
         HAIL_GENETICS_VEP_GRCH37_85_IMAGE=docker://us-docker.pkg.dev/hail-vdc/hail/hailgenetics/vep-grch37-85:deploy-123abc
         HAIL_GENETICS_VEP_GRCH38_95_IMAGE=docker://us-docker.pkg.dev/hail-vdc/hail/hailgenetics/vep-grch38-95:deploy-123abc
-        AZURE_WHEEL=/path/to/wheel/for/azure
         WEBSITE_TAR=/path/to/www.tar.gz
         bash $(basename "$0")
 EOF
@@ -36,8 +35,7 @@ retry() {
         (sleep 5 && "$@");
 }
 
-arguments="AZURE_WHEEL \
-           GITHUB_OAUTH_HEADER_FILE \
+arguments="GITHUB_OAUTH_HEADER_FILE \
            GIT_VERSION \
            HAIL_GENETICS_HAILTOP_IMAGE \
            HAIL_GENETICS_HAIL_IMAGE \
@@ -88,11 +86,6 @@ then
     exit 1
 fi
 
-if [ ! -f $WHEEL_FOR_AZURE ]
-then
-    echo "wheel for azure not found $WHEEL_FOR_AZURE"
-fi
-
 if [ ! -f python/hail/experimental/datasets.json ]
 then
     echo "datasets.json not found at python/hail/experimental/datasets.json"
@@ -169,11 +162,6 @@ retry skopeo copy $HAIL_GENETICS_VEP_GRCH38_95_IMAGE docker://us-docker.pkg.dev/
 # deploy to PyPI
 twine upload $WHEEL
 
-# deploy wheel for Azure HDInsight
-azure_wheel_url=gs://hail-common/azure-hdinsight-wheels/$(basename $AZURE_WHEEL)
-gcloud storage cp $AZURE_WHEEL $azure_wheel_url
-gcloud storage objects update $azure_wheel_url --temporary-hold
-
 # deploy datasets (annotation db) json
 datasets_json_url=gs://hail-common/annotationdb/$HAIL_VERSION/datasets.json
 gcloud storage cp python/hail/experimental/datasets.json $datasets_json_url
diff --git a/hail/src/main/resources/build-info.properties b/hail/src/main/resources/build-info.properties
new file mode 100644
index 00000000000..780c704d7ad
--- /dev/null
+++ b/hail/src/main/resources/build-info.properties
@@ -0,0 +1,7 @@
+[Build Metadata]
+user=milo
+revision=8f6797b033d2e102575c40166cf0c977e91f834e
+branch=main
+date=2024-05-10T06:35:03Z
+sparkVersion=3.3.0
+hailPipVersion=0.2.126
diff --git a/infra/gcp-broad/hail-is/global.tfvars b/infra/gcp-broad/hail-is/global.tfvars
index 4f2be4f5094..3e3248b3443 100644
--- a/infra/gcp-broad/hail-is/global.tfvars
+++ b/infra/gcp-broad/hail-is/global.tfvars
@@ -7,7 +7,8 @@ github_organization = "hail-is"
 
 # batch_gcp_regions is a JSON array of string, the names of the gcp
 # regions to schedule over in Batch. E.g. "[\"us-central1\"]"
-batch_gcp_regions = "[\"us-central1\"]"
+# Note: doesn't update the k8s secret in gcp-broad, but does impact which cloudnat resources are created.
+batch_gcp_regions = "[\"us-central1\",\"us-east1\",\"us-east4\",\"us-west1\",\"us-west2\",\"us-west3\",\"us-west4\"]"
 
 gcp_project = "hail-vdc"
 
diff --git a/infra/gcp-broad/main.tf b/infra/gcp-broad/main.tf
index 75b27ea7411..34ed0705f0a 100644
--- a/infra/gcp-broad/main.tf
+++ b/infra/gcp-broad/main.tf
@@ -48,11 +48,6 @@ variable "use_artifact_registry" {
 }
 variable artifact_registry_location {}
 
-variable deploy_ukbb {
-  type = bool
-  description = "Run the UKBB Genetic Correlation browser"
-  default = false
-}
 variable default_subnet_ip_cidr_range {}
 
 locals {
@@ -62,6 +57,7 @@ locals {
     "gcr.io/${var.gcp_project}"
   )
   docker_root_image = "${local.docker_prefix}/ubuntu:24.04"
+  dockerhub_prefix  = "${var.artifact_registry_location}-docker.pkg.dev/${var.gcp_project}/dockerhubproxy"
 }
 
 provider "google" {
@@ -508,20 +504,30 @@ resource "google_compute_address" "internal_gateway" {
   region = var.gcp_region
 }
 
-# Cloud Router for GKE node outbound NAT
-resource "google_compute_router" "gke_node_outbound_router" {
-  name    = "gke-node-outbound-router"
-  region  = var.gcp_region
-  network = google_compute_network.default.id
+# Parse batch_gcp_regions to create Cloud NAT for all regions where batch instances can be created
+locals {
+  batch_regions = jsondecode(var.batch_gcp_regions)
 }
 
-# Cloud NAT Gateway for GKE private node outbound internet access
-resource "google_compute_router_nat" "gke_node_outbound_nat" {
-  name                               = "gke-node-outbound-nat"
-  router                            = google_compute_router.gke_node_outbound_router.name
-  region                            = var.gcp_region
+# Cloud Routers for outbound NAT in all batch regions
+resource "google_compute_router" "outbound_router" {
+  for_each = toset(local.batch_regions)
+  name     = "outbound-router-${each.key}"
+  region   = each.key
+  network  = google_compute_network.default.id
+}
+
+# Cloud NAT Gateways for outbound internet access in all batch regions
+resource "google_compute_router_nat" "outbound_nat" {
+  for_each = google_compute_router.outbound_router
+  name                               = "outbound-nat-${each.key}"
+  router                            = each.value.name
+  region                            = each.key
   nat_ip_allocate_option            = "AUTO_ONLY"
   source_subnetwork_ip_ranges_to_nat = "ALL_SUBNETWORKS_ALL_IP_RANGES"
+  enable_dynamic_port_allocation     = true
+  min_ports_per_vm                  = 512
+  max_ports_per_vm                  = 16384
 
   log_config {
     enable = true
@@ -551,6 +557,42 @@ resource "google_artifact_registry_repository" "repository" {
   }
 }
 
+resource "google_artifact_registry_repository" "dockerhub_remote" {
+  provider      = google-beta
+  format        = "DOCKER"
+  mode          = "REMOTE_REPOSITORY"
+  repository_id = "dockerhubproxy"
+  location      = var.artifact_registry_location
+  cleanup_policy_dry_run = false
+
+  remote_repository_config {
+    description = "Docker Hub remote repository for Batch worker images"
+    common_repository {
+      uri = "https://registry-1.docker.io"
+    }
+  }
+
+  cleanup_policies {
+    id     = "Delete after 6h"
+    action = "DELETE"
+    condition {
+      older_than            = "21600s"
+      package_name_prefixes = []
+      tag_prefixes          = []
+      tag_state             = "ANY"
+      version_name_prefixes  = []
+    }
+  }
+
+  lifecycle {
+    # Ignore fields that are managed outside Terraform or have different representations
+    ignore_changes = [
+      remote_repository_config[0].description,
+      remote_repository_config[0].upstream_credentials,
+    ]
+  }
+}
+
 resource "google_service_account" "gcr_push" {
   account_id = "gcr-push"
   display_name = "push to gcr.io"
@@ -565,6 +607,17 @@ resource "google_artifact_registry_repository_iam_member" "artifact_registry_bat
   member = "serviceAccount:${google_service_account.batch_agent.email}"
 }
 
+# Grant all service accounts in the project read access to dockerhubproxy
+resource "google_artifact_registry_repository_iam_member" "artifact_registry_all_service_accounts_dockerhub_viewer" {
+  provider  = google-beta
+  project   = var.gcp_project
+  repository = google_artifact_registry_repository.dockerhub_remote.name
+  location  = var.artifact_registry_location
+  role      = "roles/artifactregistry.reader"
+  member    = "principalSet://cloudresourcemanager.googleapis.com/projects/${data.google_project.current.number}/type/ServiceAccount"
+}
+
+
 resource "google_artifact_registry_repository_iam_member" "artifact_registry_ci_admin" {
   provider = google-beta
   project = var.gcp_project
@@ -583,10 +636,6 @@ resource "google_artifact_registry_repository_iam_member" "artifact_registry_pus
   member = "serviceAccount:${google_service_account.gcr_push.email}"
 }
 
-module "ukbb" {
-  count = var.deploy_ukbb ? 1 : 0
-  source = "../k8s/ukbb"
-}
 
 resource "google_project_iam_custom_role" "auth_service_account_manager" {
   role_id     = "authServiceAccountManager"
diff --git a/infra/gcp/README.md b/infra/gcp/README.md
index de31bc98a3c..883f90a4828 100644
--- a/infra/gcp/README.md
+++ b/infra/gcp/README.md
@@ -125,6 +125,11 @@ export GCP_PROJECT=<gcp project name>
        display_name = "GKE Control Plane and Nodes"
      }
    ]
+
+   # Optional: Support email address to display in error pages and user-facing messages
+   # If not set, error pages will display "email support" without a link
+   # If set, error pages will display a clickable mailto link
+   support_email = "<support-email@example.com>"
    ```
 
 - You can optionally create a `/tmp/ci_config.json` file to enable CI triggered by GitHub
@@ -258,6 +263,20 @@ rm -rf .terraform terraform.lock.hcl terraform.tfstate terraform.tfstate.backup
     - `<domain>`
     - `*.<domain>`
 
+## Add a docker login for the dockerhubproxy repository (Recommended)
+
+**Note**: This step is optional but highly recommended. The repository works without authentication, but Docker Hub rate limits are likely to be hit when pulling anonymously because Artifact Registry, as a global service, reuses the same IP address across multiple users and projects.
+
+- Identify a Docker Hub account to use for upstream authentication to Docker Hub for the proxy.
+- Create a personal access token for the Docker Hub account.
+  - It can be readonly
+  - You can choose whether to allow it to pull private repositories or just use it for public repositories.
+- Add the personal access token to a Google Secret Manager secret.
+- In the Google Cloud Console, navigate to Artifact Registry → Repositories → `dockerhubproxy` → Edit → Remote repository settings.
+- Configure the repository to use the Docker Hub username and the Secret Manager secret containing the personal access token.
+
+**Note**: Terraform is configured to ignore changes to upstream credentials (via `lifecycle.ignore_changes`), so manually configured credentials will not be overwritten by subsequent Terraform runs.
+
 ## Deploy Hail to Kubernetes
 
 We can now deploy Hail to the kubernetes cluster that terraform created.
diff --git a/infra/gcp/main.tf b/infra/gcp/main.tf
index 805e6552642..bc3b35e08f7 100644
--- a/infra/gcp/main.tf
+++ b/infra/gcp/main.tf
@@ -50,12 +50,6 @@ variable "use_artifact_registry" {
   description = "pull the ubuntu image from Artifact Registry. Otherwise, GCR"
 }
 
-variable deploy_ukbb {
-  type = bool
-  description = "Run the UKBB Genetic Correlation browser"
-  default = false
-}
-
 variable "enable_master_authorized_networks" {
   type = bool
   description = "Enable master authorized networks configuration for GKE cluster"
@@ -71,6 +65,12 @@ variable "master_authorized_networks" {
   default = []
 }
 
+variable "support_email" {
+  type        = string
+  description = "Support email address to display in error pages and user-facing messages"
+  default     = ""
+}
+
 locals {
   docker_prefix = (
     var.use_artifact_registry ?
@@ -78,6 +78,7 @@ locals {
     "gcr.io/${var.gcp_project}"
   )
   docker_root_image = "${local.docker_prefix}/ubuntu:24.04"
+  dockerhub_prefix  = "${var.gcp_location}-docker.pkg.dev/${var.gcp_project}/dockerhubproxy"
 }
 
 data "sops_file" "terraform_sa_key_sops" {
@@ -395,21 +396,31 @@ resource "google_compute_address" "internal_gateway" {
   region = var.gcp_region
 }
 
-# Cloud Router for GKE node outbound NAT
-resource "google_compute_router" "gke_node_outbound_router" {
-  name    = "gke-node-outbound-router"
-  region  = var.gcp_region
-  network = google_compute_network.default.id
+# Parse batch_gcp_regions to create Cloud NAT for all regions where batch instances can be created
+locals {
+  batch_regions = jsondecode(var.batch_gcp_regions)
+}
+
+# Cloud Routers for outbound NAT in all batch regions
+resource "google_compute_router" "outbound_router" {
+  for_each = toset(local.batch_regions)
+  name     = "outbound-router-${each.key}"
+  region   = each.key
+  network  = google_compute_network.default.id
 }
 
-# Cloud NAT Gateway for GKE private node outbound internet access
-resource "google_compute_router_nat" "gke_node_outbound_nat" {
-  name                               = "gke-node-outbound-nat"
-  router                            = google_compute_router.gke_node_outbound_router.name
-  region                            = var.gcp_region
+# Cloud NAT Gateways for outbound internet access in all batch regions
+resource "google_compute_router_nat" "outbound_nat" {
+  for_each = google_compute_router.outbound_router
+  name                               = "outbound-nat-${each.key}"
+  router                            = each.value.name
+  region                            = each.key
   nat_ip_allocate_option            = "AUTO_ONLY"
   source_subnetwork_ip_ranges_to_nat = "ALL_SUBNETWORKS_ALL_IP_RANGES"
-  
+  enable_dynamic_port_allocation     = true
+  min_ports_per_vm                  = 512
+  max_ports_per_vm                  = 16384
+
   log_config {
     enable = true
     filter = "ERRORS_ONLY"
@@ -429,7 +440,7 @@ resource "kubernetes_secret" "global_config" {
     name = "global-config"
   }
 
-  data = {
+  data = merge({
     cloud = "gcp"
     batch_gcp_regions = var.batch_gcp_regions
     batch_logs_bucket = module.batch_logs.name  # Deprecated
@@ -445,11 +456,14 @@ resource "kubernetes_secret" "global_config" {
     gcp_region = var.gcp_region
     gcp_zone = var.gcp_zone
     docker_prefix = local.docker_prefix
+    dockerhub_prefix = local.dockerhub_prefix
     internal_ip = google_compute_address.internal_gateway.address
     ip = google_compute_address.gateway.address
     kubernetes_server_url = "https://${google_container_cluster.vdc.endpoint}"
     organization_domain = var.organization_domain
-  }
+  }, var.support_email != "" ? {
+    support_email = var.support_email
+  } : {})
 }
 
 resource "google_sql_ssl_cert" "root_client_cert" {
@@ -511,6 +525,41 @@ resource "google_artifact_registry_repository" "repository" {
   location = var.gcp_location
 }
 
+resource "google_artifact_registry_repository" "dockerhub_remote" {
+  provider      = google-beta
+  format        = "DOCKER"
+  mode          = "REMOTE_REPOSITORY"
+  repository_id = "dockerhubproxy"
+  location      = var.gcp_location
+  cleanup_policy_dry_run = false
+
+  remote_repository_config {
+    description = "Docker Hub remote repository for Batch worker images"
+    common_repository {
+      uri = "https://registry-1.docker.io"
+    }
+  }
+
+  cleanup_policies {
+    id     = "Delete after 6h"
+    action = "DELETE"
+    condition {
+      older_than            = "21600s"
+      package_name_prefixes = []
+      tag_prefixes          = []
+      tag_state             = "ANY"
+      version_name_prefixes  = []
+    }
+  }
+
+  lifecycle {
+    # Ignore fields that are managed outside Terraform or have different representations
+    ignore_changes = [
+      remote_repository_config[0].upstream_credentials,
+    ]
+  }
+}
+
 resource "google_service_account" "gcr_push" {
   account_id = "gcr-push"
   display_name = "push to gcr.io"
@@ -529,6 +578,17 @@ resource "google_artifact_registry_repository_iam_member" "artifact_registry_bat
   member = "serviceAccount:${google_service_account.batch_agent.email}"
 }
 
+# Grant all service accounts in the project read access to dockerhubproxy
+resource "google_artifact_registry_repository_iam_member" "artifact_registry_all_service_accounts_dockerhub_viewer" {
+  provider  = google-beta
+  project   = var.gcp_project
+  repository = google_artifact_registry_repository.dockerhub_remote.name
+  location  = var.gcp_location
+  role      = "roles/artifactregistry.reader"
+  member    = "principalSet://cloudresourcemanager.googleapis.com/projects/${data.google_project.current.number}/type/ServiceAccount"
+}
+
+
 resource "google_artifact_registry_repository_iam_member" "artifact_registry_ci_admin" {
   provider = google-beta
   project = var.gcp_project
diff --git a/infra/k8s/ukbb/main.tf b/infra/k8s/ukbb/main.tf
deleted file mode 100644
index e1f3a367eb8..00000000000
--- a/infra/k8s/ukbb/main.tf
+++ /dev/null
@@ -1,45 +0,0 @@
-resource "kubernetes_namespace" "ukbb_rg" {
-  metadata {
-    name = "ukbb-rg"
-  }
-}
-
-resource "kubernetes_service" "ukbb_rb_browser" {
-  metadata {
-    name = "ukbb-rg-browser"
-    namespace = kubernetes_namespace.ukbb_rg.metadata[0].name
-    labels = {
-      app = "ukbb-rg-browser"
-    }
-  }
-  spec {
-    port {
-      port = 80
-      protocol = "TCP"
-      target_port = 80
-    }
-    selector = {
-      app = "ukbb-rg-browser"
-    }
-  }
-}
-
-resource "kubernetes_service" "ukbb_rb_static" {
-  metadata {
-    name = "ukbb-rg-static"
-    namespace = kubernetes_namespace.ukbb_rg.metadata[0].name
-    labels = {
-      app = "ukbb-rg-static"
-    }
-  }
-  spec {
-    port {
-      port = 80
-      protocol = "TCP"
-      target_port = 80
-    }
-    selector = {
-      app = "ukbb-rg-static"
-    }
-  }
-}
diff --git a/monitoring/monitoring/templates/billing.html b/monitoring/monitoring/templates/billing.html
index 124f9bd24bb..1a94c499610 100644
--- a/monitoring/monitoring/templates/billing.html
+++ b/monitoring/monitoring/templates/billing.html
@@ -1,8 +1,8 @@
 {% extends "layout.html" %}
 {% block title %}Billing{% endblock %}
 {% block head %}
-    <script src="{{ base_path }}/common_static/search_bar.js"></script>
-    <script src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
+    <script defer src="{{ base_path }}/common_static/search_bar.js"></script>
+    <script defer src="{{ base_path }}/common_static/focus_on_keyup.js"></script>
 {% endblock %}
 {% block content %}
 <div class="flex-col-align-left">
@@ -57,7 +57,7 @@ <h1>Compute Engine Costs by Source</h1>
 
 <h1>Costs by Product</h1>
 <div class="searchbar-table">
-  <input type="text" id="searchBar" onkeyup="searchTable('productCost', 'searchBar')" placeholder="Search terms...">
+  <input type="text" id="searchBar" name="searchbar-input" data-table-id="productCost" placeholder="Search terms...">
   <table id="productCost" class="data-table">
       <thead>
       <tr>
diff --git a/ukbb-rg/.gitignore b/ukbb-rg/.gitignore
deleted file mode 100644
index 1269488f7fb..00000000000
--- a/ukbb-rg/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-data
diff --git a/ukbb-rg/Dockerfile.browser b/ukbb-rg/Dockerfile.browser
deleted file mode 100644
index 272cba1ff84..00000000000
--- a/ukbb-rg/Dockerfile.browser
+++ /dev/null
@@ -1,28 +0,0 @@
-ARG DOCKER_PREFIX=docker.io
-FROM $DOCKER_PREFIX/ubuntu:22.04
-
-ENV DEBIAN_FRONTEND=noninteractive
-RUN apt-get update && \
-  apt-get -y install \
-    tzdata \
-    r-base \
-    wget \
-    gdebi-core && \
-  rm -rf /var/lib/apt/lists/*
-
-RUN R -e "install.packages(c('shiny', 'rmarkdown', 'data.table', 'formattable', 'dplyr', 'DT', 'shinyWidgets', 'shinyjs'), repos='https://cran.rstudio.com/', Ncpus=4)"
-
-RUN wget -nv -O shiny-server-1.5.9.923-amd64.deb https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.9.923-amd64.deb && \
- gdebi -n shiny-server-1.5.9.923-amd64.deb && \
- rm -f shiny-server-1.5.9.923-amd64.deb && \
- rm -r /srv/shiny-server/index.html /srv/shiny-server/sample-apps
-
-COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
-COPY app/app.R /srv/shiny-server/rg_browser/
-COPY app/www/rainbowvis.js /srv/shiny-server/rg_browser/www/rainbowvis.js
-
-RUN ln -s /ukbb-rg-browser/Rdata_outputs /srv/shiny-server/rg_browser/Rdata_outputs
-
-EXPOSE 3838
-
-CMD ["shiny-server"]
diff --git a/ukbb-rg/Dockerfile.static b/ukbb-rg/Dockerfile.static
deleted file mode 100644
index fa84ed847ba..00000000000
--- a/ukbb-rg/Dockerfile.static
+++ /dev/null
@@ -1,14 +0,0 @@
-ARG DOCKER_PREFIX=docker.io
-FROM $DOCKER_PREFIX/ubuntu:22.04
-
-RUN apt-get update -y && \
-    apt-get install -y nginx && \
-    rm -rf /var/lib/apt/lists/*
-
-RUN rm -f /etc/nginx/sites-enabled/default
-ADD static.nginx.conf /etc/nginx/conf.d
-
-RUN ln -sf /dev/stdout /var/log/nginx/access.log
-RUN ln -sf /dev/stderr /var/log/nginx/error.log
-
-CMD ["nginx", "-g", "daemon off;"]
diff --git a/ukbb-rg/Makefile b/ukbb-rg/Makefile
deleted file mode 100644
index 7c0bd64ef4d..00000000000
--- a/ukbb-rg/Makefile
+++ /dev/null
@@ -1,40 +0,0 @@
-include ../config.mk
-
-UKBB_RG_STATIC_IMAGE := $(DOCKER_PREFIX)/ukbb-rg-static:$(TOKEN)
-UKBB_RG_BROWSER_IMAGE := $(DOCKER_PREFIX)/ukbb-rg-browser:$(TOKEN)
-
-.PHONY: build
-build:
-	ls app/app.R app/www/rainbowvis.js # read the README
-
-	python3 ../ci/jinja2_render.py '{"docker_prefix":"$(DOCKER_PREFIX)"}' Dockerfile.static Dockerfile.static.out
-	../docker-build.sh . Dockerfile.static.out $(UKBB_RG_STATIC_IMAGE)
-
-	python3 ../ci/jinja2_render.py '{"docker_prefix":"$(DOCKER_PREFIX)"}' Dockerfile.browser Dockerfile.browser.out
-	../docker-build.sh . Dockerfile.browser.out $(UKBB_RG_BROWSER_IMAGE)
-
-.PHONY: deploy
-deploy: build
-	python3 ../ci/jinja2_render.py '{"docker_prefix":"$(DOCKER_PREFIX)","static_image":"$(UKBB_RG_STATIC_IMAGE)","browser_image":"$(UKBB_RG_BROWSER_IMAGE)"}' deployment.yaml deployment.yaml.out
-	kubectl apply -n ukbb-rg -f deployment.yaml.out
-
-update-ukbb-rg-browser-files:
-	mkdir -p data
-	mkdir -p data/Rdata_outputs
-	[ -e data/Rdata_outputs ] \
-    || gcloud storage cp -r gs://rg-website/Rdata_outputs/ data/Rdata_outputs
-	kubectl exec ukbb-rg-browser-0 -n ukbb-rg -- /bin/sh -c '[ -e /ukbb-rg-browser/Rdata_outputs ]' \
-    || kubectl cp Rdata_outputs ukbb-rg/ukbb-rg-browser:/ukbb-rg-browser/Rdata_outputs
-
-update-ukbb-rg-static-files:
-	mkdir -p data
-	mkdir -p data/docs
-	[ -e data/docs ] \
-    || gcloud storage cp -r gs://rg-website/docs/ data/docs
-	mkdir -p data/site_libs
-	[ -e data/site_libs ] \
-    || gcloud storage cp -r gs://rg-website/site_libs/ data/site_libs # >2GB of data
-	kubectl exec ukbb-rg-static-0 -n ukbb-rg -- /bin/sh -c '[ -e /ukbb-rg-static/rg_summary_102.html ]' \
-    || kubectl cp docs/rg_summary_102.html ukbb-rg/ukbb-rg-static:/ukbb-rg-static/rg_summary_102.html
-	kubectl exec ukbb-rg-static-0 -n ukbb-rg -- /bin/sh -c '[ -e /ukbb-rg-static/site_libs ]' \
-    || kubectl cp site_libs ukbb-rg/ukbb-rg-static:/ukbb-rg-static/site_libs
diff --git a/ukbb-rg/README b/ukbb-rg/README
deleted file mode 100644
index dab0e351176..00000000000
--- a/ukbb-rg/README
+++ /dev/null
@@ -1,34 +0,0 @@
-About
------
-
-This is the UKBB genetic correlation browser.  It consists of two
-stateful sets deployed in the ukbb-rg namespace:
-
- - ukbb-rg-static, which runs nginx and serves static content, and
- - ukbb-rg-browser, which runs a R Shiny server
-
-Updating
---------
-
-The ukbb-rg browser, beyond the contents of this directory, depends on
-four sets of files:
-
- - docs
- - site_libs
- - Rdata_outputs
- - app
-
-app consists of two files:
-
- - app/app.R
- - app/www/rainbowvis.js
-
-which must be copied into ./app in this directory before running "make deploy"
-to update the images. You can find these files [in Duncan's GitHub repository at
-`/r2_browser`](https://github.com/astheeggeggs/UKBB_ldsc_r2/tree/master/r2_browser).
-
-The other three sets of files should already be present on the persistent disks
-associated with the stateful set. If they are not, you can upload them with
-`make update-ukbb-rg-browser-files` and `make
-update-ukbb-rg-static-files`. These make targets only work for stateful sets of
-size one.
diff --git a/ukbb-rg/deployment.yaml b/ukbb-rg/deployment.yaml
deleted file mode 100644
index 7fdc0e7edef..00000000000
--- a/ukbb-rg/deployment.yaml
+++ /dev/null
@@ -1,255 +0,0 @@
-apiVersion: v1
-kind: Namespace
-metadata:
-  name: ukbb-rg
----
-apiVersion: storage.k8s.io/v1
-kind: StorageClass
-metadata:
-  name: ssd
-provisioner: kubernetes.io/gce-pd
-parameters:
-  type: pd-ssd
----
-apiVersion: apps/v1
-kind: StatefulSet
-metadata:
-  name: ukbb-rg-static
-  namespace: ukbb-rg
-  labels:
-    name: ukbb-rg-static
-spec:
-  serviceName: "ukbb-rg-static"
-  selector:
-    matchLabels:
-      app: ukbb-rg-static
-  replicas: 1
-  template:
-    metadata:
-      labels:
-        app: ukbb-rg-static
-    spec:
-      nodeSelector:
-        preemptible: "false"
-      containers:
-       - name: ukbb-rg-static
-         image: {{ static_image }}
-         imagePullPolicy: Always
-         resources:
-           requests:
-             cpu: "100m"
-             memory: "200M"
-           limits:
-             cpu: "1"
-             memory: "1G"
-         ports:
-          - containerPort: 443
-            protocol: TCP
-         volumeMounts:
-          - mountPath: "/ukbb-rg-static"
-            name: ukbb-rg-static-storage
-          - name: ssl-config-ukbb-rg
-            mountPath: /ssl-config
-            readOnly: true
-      volumes:
-       - name: ssl-config-ukbb-rg
-         secret:
-           optional: false
-           secretName: ssl-config-ukbb-rg
-  volumeClaimTemplates:
-    - metadata:
-        name: ukbb-rg-static-storage
-        namespace: ukbb-rg-static
-      spec:
-        accessModes:
-          - ReadWriteOnce
-        storageClassName: ssd
-        resources:
-          requests:
-            storage: 20Gi
----
-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: tls-sidecar-envoy-config
-data:
-  envoy.yaml: |
-    static_resources:
-      listeners:
-      - address:
-          socket_address:
-            address: 0.0.0.0
-            port_value: 8443
-        filter_chains:
-        - filters:
-          - name: envoy.filters.network.http_connection_manager
-            typed_config:
-              "@type": type.googleapis.com/envoy.extensions.filters.network.http_connection_manager.v3.HttpConnectionManager
-              codec_type: AUTO
-              stat_prefix: ingress_http
-              route_config:
-                name: local_route
-                virtual_hosts:
-                  - name: ukbb-rg-browser
-                    domains: ["*"]
-                    routes:
-                      - match:
-                          prefix: "/"
-                        route:
-                          timeout: 0s
-                          cluster: ukbb-rg-browser
-              http_filters:
-                - name: envoy.filters.http.router
-                  typed_config:
-                    "@type": type.googleapis.com/envoy.extensions.filters.http.router.v3.Router
-          transport_socket:
-            name: envoy.transport_sockets.tls
-            typed_config:
-              "@type": type.googleapis.com/envoy.extensions.transport_sockets.tls.v3.DownstreamTlsContext
-              common_tls_context:
-                tls_certificates:
-                - certificate_chain:
-                    filename: /ssl-config/ukbb-rg-cert.pem
-                  private_key:
-                    filename: /ssl-config/ukbb-rg-key.pem
-      clusters:
-      - name: ukbb-rg-browser
-        type: STRICT_DNS
-        lb_policy: ROUND_ROBIN
-        load_assignment:
-          cluster_name: ukbb-rg-browser
-          endpoints:
-          - lb_endpoints:
-            - endpoint:
-                address:
-                  socket_address:
-                    address: 127.0.0.1
-                    port_value: 3838
-    admin:
-      address:
-        socket_address:
-          address: 127.0.0.1
-          port_value: 8001
----
-apiVersion: apps/v1
-kind: StatefulSet
-metadata:
-  name: ukbb-rg-browser
-  namespace: ukbb-rg
-  labels:
-    name: ukbb-rg-browser
-spec:
-  serviceName: "ukbb-rg-browser"
-  selector:
-    matchLabels:
-      app: ukbb-rg-browser
-  replicas: 1
-  template:
-    metadata:
-      labels:
-        app: ukbb-rg-browser
-    spec:
-      nodeSelector:
-        preemptible: "false"
-      containers:
-       - name: ukbb-rg-browser
-         image: {{ browser_image }}
-         imagePullPolicy: Always
-         resources:
-           requests:
-             cpu: "100m"
-             memory: "200M"
-           limits:
-             cpu: "1"
-             memory: "1G"
-         ports:
-          - containerPort: 3838
-            protocol: TCP
-         volumeMounts:
-          - mountPath: "/ukbb-rg-browser"
-            name: ukbb-rg-browser-storage
-         readinessProbe: # shiny loads data on first request, this takes ~15 seconds
-           httpGet:
-             path: /rg_browser/
-             port: 3838
-           initialDelaySeconds: 1
-           periodSeconds: 30
-           timeoutSeconds: 30
-       - name: envoy
-         image: "{{ docker_prefix }}/envoyproxy/envoy:v1.33.0"
-         command:
-           - /usr/local/bin/envoy
-           - --config-path
-           - /etc/envoy/envoy.yaml
-           - --concurrency
-           - "2"
-         resources:
-           requests:
-             cpu: "20m"
-             memory: "20M"
-           limits:
-             cpu: "1"
-             memory: "1G"
-         ports:
-          - containerPort: 8443
-         volumeMounts:
-          - name: ssl-config-ukbb-rg
-            mountPath: /ssl-config
-            readOnly: true
-          - name: tls-sidecar-envoy-config
-            mountPath: /etc/envoy
-            readOnly: true
-         readinessProbe:
-           tcpSocket:
-             port: 8443
-           initialDelaySeconds: 5
-           periodSeconds: 5
-      volumes:
-       - name: ssl-config-ukbb-rg
-         secret:
-           optional: false
-           secretName: ssl-config-ukbb-rg
-       - name: tls-sidecar-envoy-config
-         configMap:
-           name: tls-sidecar-envoy-config
-  volumeClaimTemplates:
-    - metadata:
-        name: ukbb-rg-browser-storage
-        namespace: ukbb-rg-browser
-      spec:
-        accessModes:
-          - ReadWriteOnce
-        storageClassName: ssd
-        resources:
-          requests:
-            storage: 20Gi
----
-apiVersion: v1
-kind: Service
-metadata:
-  name: ukbb-rg-static
-  namespace: ukbb-rg
-  labels:
-    app: ukbb-rg-static
-spec:
-  ports:
-  - port: 443
-    protocol: TCP
-    targetPort: 443
-  selector:
-    app: ukbb-rg-static
----
-apiVersion: v1
-kind: Service
-metadata:
-  name: ukbb-rg-browser
-  namespace: ukbb-rg
-  labels:
-    app: ukbb-rg-browser
-spec:
-  ports:
-  - port: 443
-    protocol: TCP
-    targetPort: 8443
-  selector:
-    app: ukbb-rg-browser
diff --git a/ukbb-rg/shiny-server.conf b/ukbb-rg/shiny-server.conf
deleted file mode 100644
index 2e87d6aaace..00000000000
--- a/ukbb-rg/shiny-server.conf
+++ /dev/null
@@ -1,27 +0,0 @@
-# Instruct Shiny Server to run applications as the user "shiny"
-run_as shiny;
-
-# Define a server that listens on port 3838
-server {
-  listen 3838;
-
-  location /rg_browser/static {
-    site_dir /srv/shiny-server/static;
-    log_dir /var/log/shiny-server;
-  }
-  
-  # Define a location at the base URL
-  location /rg_browser {
-
-    # Host the directory of Shiny Apps stored in this directory
-    site_dir /srv/shiny-server/rg_browser;
-
-    # Log all Shiny output to files in this directory
-    log_dir /var/log/shiny-server;
-
-    # When a user visits the base URL rather than a particular application,
-    # an index of the applications available in this directory will be shown.
-    directory_index on;
-  }
-
-}
diff --git a/ukbb-rg/static.nginx.conf b/ukbb-rg/static.nginx.conf
deleted file mode 100644
index 6e8270d9a20..00000000000
--- a/ukbb-rg/static.nginx.conf
+++ /dev/null
@@ -1,16 +0,0 @@
-server {
-    server_name ukbb-rg;
-
-    include /ssl-config/ssl-config-http.conf;
-
-    location = /health {
-        return 200;
-    }
-
-    location / {
-        root /ukbb-rg-static;
-    }
-
-    listen 443 ssl;
-    listen [::]:443 ssl;
-}
diff --git a/web_common/pinned-requirements.txt b/web_common/pinned-requirements.txt
index bdfa04834cc..1e03d8607d9 100644
--- a/web_common/pinned-requirements.txt
+++ b/web_common/pinned-requirements.txt
@@ -6,7 +6,7 @@ aiohappyeyeballs==2.6.1
     #   -c web_common/../hail/python/dev/pinned-requirements.txt
     #   -c web_common/../hail/python/pinned-requirements.txt
     #   aiohttp
-aiohttp==3.13.2
+aiohttp==3.13.3
     # via
     #   -c web_common/../gear/pinned-requirements.txt
     #   -c web_common/../hail/python/dev/pinned-requirements.txt
@@ -58,7 +58,7 @@ markupsafe==3.0.3
     #   -c web_common/../hail/python/dev/pinned-requirements.txt
     #   -c web_common/../hail/python/pinned-requirements.txt
     #   jinja2
-multidict==6.7.0
+multidict==6.7.1
     # via
     #   -c web_common/../gear/pinned-requirements.txt
     #   -c web_common/../hail/python/dev/pinned-requirements.txt
diff --git a/web_common/web_common/static/focus_on_keyup.js b/web_common/web_common/static/focus_on_keyup.js
index e62a959ae80..f610ef60c1f 100644
--- a/web_common/web_common/static/focus_on_keyup.js
+++ b/web_common/web_common/static/focus_on_keyup.js
@@ -5,3 +5,5 @@ function focusOnSlash(name) {
     }
   }
 }
+
+focusOnSlash("prsSearchBar");
diff --git a/web_common/web_common/static/js/swagger/index.js b/web_common/web_common/static/js/swagger/index.js
new file mode 100644
index 00000000000..77cdac2c4bb
--- /dev/null
+++ b/web_common/web_common/static/js/swagger/index.js
@@ -0,0 +1,31 @@
+const csrfToken = document.head.querySelector('meta[name="csrf"]')?.getAttribute('value') || '';
+const basePath = document.head.querySelector('meta[name="base-path"]')?.getAttribute('value') || '';
+
+if (Object.hasOwn(window, "SwaggerUIBundle") && Object.hasOwn(window, "SwaggerUIStandalonePreset")) {
+    window.onload = function() {
+        window.ui = window.SwaggerUIBundle({
+            url: `${basePath}/openapi.yaml`,
+            dom_id: '#swagger-ui',
+            deepLinking: true,
+            presets: [
+                window.SwaggerUIBundle.presets.apis,
+                window.SwaggerUIStandalonePreset
+            ],
+            plugins: [
+                window.SwaggerUIBundle.plugins.DownloadUrl
+            ],
+            layout: "StandaloneLayout",
+            requestInterceptor: function(request) {
+                if (csrfToken) {
+                    // Add CSRF token to request headers
+                    if (!request.headers) {
+                        request.headers = {};
+                    }
+                    request.headers['X-CSRF-Token'] = csrfToken;
+                }
+
+                return request;
+            }
+        });
+    };
+}
diff --git a/web_common/web_common/static/search_bar.js b/web_common/web_common/static/search_bar.js
index b19388a8dc1..15b823ffcf9 100644
--- a/web_common/web_common/static/search_bar.js
+++ b/web_common/web_common/static/search_bar.js
@@ -22,3 +22,10 @@ function searchTable(table_name, search_bar_name) {
     }
   }
 }
+
+document.getElementsByName("searchbar-input").forEach(searchBarInput => {
+    var tableId = searchBarInput.dataset.tableId;
+    if (tableId && searchBarInput.id) {
+        searchBarInput.addEventListener("keyup", (_e) => searchTable(tableId, searchBarInput.id));
+    }
+});
diff --git a/web_common/web_common/templates/swagger/index.html b/web_common/web_common/templates/swagger/index.html
index e5ea3271301..36e3db0d009 100644
--- a/web_common/web_common/templates/swagger/index.html
+++ b/web_common/web_common/templates/swagger/index.html
@@ -3,6 +3,8 @@
 <html lang="en">
   <head>
     <meta charset="UTF-8">
+    <meta name="csrf" value="{{ csrf_token }}" />
+    <meta name="base-path" value="{{ base_path }}" />
     <title>Swagger UI</title>
     <link rel="stylesheet" type="text/css" href="{{ base_path }}/common_static/lib/swagger/swagger-ui.css" />
     <link rel="stylesheet" type="text/css" href="{{ base_path }}/common_static/lib/swagger/index.css" />
@@ -14,36 +16,6 @@
     <div id="swagger-ui"></div>
     <script src="{{ base_path }}/common_static/lib/swagger/swagger-ui-bundle.js" charset="UTF-8"> </script>
     <script src="{{ base_path }}/common_static/lib/swagger/swagger-ui-standalone-preset.js" charset="UTF-8"> </script>
-    <script>
-      window.onload = function() {
-        window.ui = SwaggerUIBundle({
-          url: '{{ base_path }}/openapi.yaml',
-          dom_id: '#swagger-ui',
-          deepLinking: true,
-          presets: [
-            SwaggerUIBundle.presets.apis,
-            SwaggerUIStandalonePreset
-          ],
-          plugins: [
-            SwaggerUIBundle.plugins.DownloadUrl
-          ],
-          layout: "StandaloneLayout",
-          requestInterceptor: function(request) {
-            // Get CSRF token from template variable
-            const csrfToken = "{{ csrf_token }}";
-
-            if (csrfToken) {
-              // Add CSRF token to request headers
-              if (!request.headers) {
-                request.headers = {};
-              }
-              request.headers['X-CSRF-Token'] = csrfToken;
-            }
-
-            return request;
-          }
-        });
-      };
-    </script>
+    <script defer src="{{ base_path }}/common_static/js/swagger/index.js"></script>
   </body>
 </html>
diff --git a/web_common/web_common/templates/utils.html b/web_common/web_common/templates/utils.html
index 3819982ae55..c2d84668508 100644
--- a/web_common/web_common/templates/utils.html
+++ b/web_common/web_common/templates/utils.html
@@ -91,6 +91,14 @@
 </a>
 {% endmacro %}
 
+{% macro auto_refresh() %}
+<div id="auto-refresh" class="flex items-center space-x-1 text-sm text-zinc-500 pt-1">
+  <input type="checkbox" id="auto-refresh-toggle" checked class="cursor-pointer">
+  <span>Auto-refresh page </span>
+  <span id="auto-refresh-detail"></span>
+</div>
+{% endmacro %}
+
 {% macro truncated_link(href, text) %}
 <a class='block hover:cursor-pointer hover:text-sky-600 hover:underline underline-offset-2 truncating-text'  href="{{ href }}">
   {{ text }}
diff --git a/web_common/web_common/web_common.py b/web_common/web_common/web_common.py
index 8f3c3cb664d..a183d337e2d 100644
--- a/web_common/web_common/web_common.py
+++ b/web_common/web_common/web_common.py
@@ -10,6 +10,7 @@
 from aiohttp import web
 
 from gear import UserData, new_csrf_token
+from gear.cloud_config import get_global_config
 from hailtop.config import get_deploy_config
 
 deploy_config = get_deploy_config()
@@ -60,6 +61,12 @@ def set_message(session, text, type):
 
 
 def base_context(session, userdata, service):
+    try:
+        global_config = get_global_config()
+        support_email = global_config.get('support_email', '')
+    except (FileNotFoundError, OSError):
+        # Fallback to empty if global config is not available (e.g., local development)
+        support_email = ''
     context = {
         'base_path': deploy_config.base_path(service),
         'base_url': deploy_config.external_url(service, ''),
@@ -70,6 +77,7 @@ def base_context(session, userdata, service):
         'ci_base_url': deploy_config.external_url('ci', ''),
         'grafana_base_url': deploy_config.external_url('grafana', ''),
         'monitoring_base_url': deploy_config.external_url('monitoring', ''),
+        'support_email': support_email,
         'userdata': userdata,
     }
     if 'message' in session:
@@ -83,6 +91,8 @@ async def render_template(
     userdata: Optional[UserData],
     file: str,
     page_context: Dict[str, Any],
+    *,
+    status_code: int = 200,
 ) -> web.Response:
     if request.headers.get('x-hail-return-jinja-context'):
         if userdata and userdata['is_developer']:
@@ -100,7 +110,7 @@ async def render_template(
     context['use_tailwind'] = service in TAILWIND_SERVICES
     context['csrf_token'] = csrf_token
 
-    response = aiohttp_jinja2.render_template(file, request, context)
+    response = aiohttp_jinja2.render_template(file, request, context, status=status_code)
     response.set_cookie('_csrf', csrf_token, secure=True, httponly=True, samesite='strict')
     return response
 
@@ -129,7 +139,7 @@ async def wrapped(request, *args, **kwargs):
         default_src = 'default-src \'self\';'
         style_src = f'style-src \'self\' \'unsafe-inline\' {extra_style} fonts.googleapis.com fonts.gstatic.com;'
         font_src = 'font-src \'self\' fonts.gstatic.com;'
-        script_src = f'script-src \'self\' \'unsafe-inline\' {extra_script} cdn.jsdelivr.net cdn.plot.ly;'
+        script_src = f'script-src \'self\' {extra_script} cdn.jsdelivr.net cdn.plot.ly;'
         img_src = f'img-src \'self\' {extra_img};'
         frame_ancestors = 'frame-ancestors \'self\';'