diff --git a/.github/workflows/README.md b/.github/workflows/README.md
index c37cf24d..7ef7accc 100644
--- a/.github/workflows/README.md
+++ b/.github/workflows/README.md
@@ -13,34 +13,47 @@ This directory contains CI/CD workflows for the DeepWork project. We use GitHub'
 
 ## Merge Queue Strategy
 
+All workflows explicitly target the `main` branch for both `pull_request` and `merge_group` triggers to ensure proper execution in the merge queue.
+
 We use a skip pattern so the same required checks pass in both PR and merge queue contexts:
 
-| Workflow | On PRs | In Merge Queue |
-|----------|--------|----------------|
-| **Validate** | Runs | Runs |
-| **Integration Tests** | Skipped (passes) | Runs |
-| **E2E Tests** | Skipped (passes) | Runs |
-| **CLA Check** | Runs | Skipped (passes) |
+| Workflow | On PRs | In Merge Queue | Manual Trigger |
+|----------|--------|----------------|----------------|
+| **Validate** | Runs | Runs | Runs |
+| **Integration Tests** | Skipped (passes) | Runs | Runs |
+| **E2E Tests** | Skipped (passes) | Runs | Runs |
+| **CLA Check** | Runs | Skipped (passes) | Skipped (passes) |
 
 ### How It Works
 
+All workflows specify explicit branch targeting:
+
+```yaml
+on:
+  pull_request:
+    branches: [main]
+  merge_group:
+    branches: [main]
+  workflow_dispatch:  # Enables manual triggering for testing
+```
+
 Jobs/steps use `if: github.event_name == 'merge_group'` conditions to control execution:
 
 ```yaml
-# Job that only runs in merge queue (skipped on PRs)
+# Job that only runs in merge queue and manual dispatch (skipped on PRs)
 jobs:
   expensive-tests:
     if: github.event_name == 'merge_group' || github.event_name == 'workflow_dispatch'
     ...
 
-# Step that skips in merge queue (runs on PRs only)
-steps:
-  - name: CLA Check
-    if: github.event_name != 'merge_group'
+# Job that skips in merge queue and manual dispatch (runs on PRs only)
+jobs:
+  cla-check:
+    if: github.event_name != 'merge_group' && github.event_name != 'workflow_dispatch'
     ...
 ```
 
-When a job/step is skipped due to an `if` condition, GitHub treats it as a successful check. This allows:
+When a job is skipped due to an `if` condition, GitHub treats it as a successful check. This allows:
 
 - **Fast PR feedback**: Only lint + unit tests run on every push
 - **Thorough merge validation**: Expensive integration/e2e tests run in merge queue before merging
@@ -50,31 +63,38 @@ When a job/step is skipped due to an `if` condition, GitHub treats it as a succe
 
 In GitHub branch protection rules, require these checks:
 - `Validate / tests`
-- `Claude Code Integration Test / validate-generation`
-- `Claude Code Integration Test / claude-code-e2e`
-- `CLA Assistant / cla-check`
+- `Claude Code Integration Test / pr-check` (for PRs)
+- `Claude Code Integration Test / validate-generation` (for merge queue)
+- `Claude Code Integration Test / claude-code-e2e` (for merge queue)
+- `CLA Assistant / merge-queue-pass` (for merge queue)
+- `CLA Assistant / cla-check` (for PRs)
 
 All checks will pass in both PR and merge queue contexts (either by running or by being skipped).
 
+**Note**: The explicit branch targeting in `merge_group` triggers is critical for workflows to run properly in the merge queue. Without this, GitHub may not trigger the workflows and they will remain in "expected" state.
+
 ## Workflow Details
 
 ### validate.yml
-- **Triggers**: `pull_request`, `merge_group`
+- **Triggers**: `pull_request` (main), `merge_group` (main), `workflow_dispatch`
 - **Jobs**: `tests` - runs ruff format/lint checks and pytest unit tests
-- Runs on every PR and in merge queue
+- Runs on every PR, in merge queue, and can be manually triggered
 
 ### claude-code-test.yml
-- **Triggers**: `pull_request`, `merge_group`, `workflow_dispatch`
+- **Triggers**: `pull_request` (main), `merge_group` (main), `workflow_dispatch`
 - **Jobs**:
+  - `pr-check`: Runs on PRs only, always passes (lightweight check)
   - `validate-generation`: Tests command generation from fixtures (no API key needed)
   - `claude-code-e2e`: Full end-to-end test with Claude Code CLI (requires `ANTHROPIC_API_KEY`)
-- Both jobs skip on PRs, run in merge queue and manual dispatch
+- `validate-generation` and `claude-code-e2e` skip on PRs, run in merge queue and manual dispatch
 
 ### cla.yml
-- **Triggers**: `pull_request_target`, `issue_comment`, `merge_group`
-- **Jobs**: `cla-check` - verifies contributors have signed the CLA
-- Runs on PRs, skips in merge queue (CLA already verified)
+- **Triggers**: `pull_request_target`, `issue_comment`, `merge_group` (main), `workflow_dispatch`
+- **Jobs**: 
+  - `merge-queue-pass`: Runs on merge queue and manual dispatch, always passes
+  - `cla-check`: Verifies contributors have signed the CLA
+- `cla-check` runs on PRs, skips in merge queue and manual dispatch (CLA already verified)
 
 ### release.yml
-- **Triggers**: Tags matching `v*`
+- **Triggers**: `release` (published)
 - **Jobs**: Builds and publishes to PyPI
diff --git a/.github/workflows/cla.yml b/.github/workflows/cla.yml
index 118f7e8b..b1940f21 100644
--- a/.github/workflows/cla.yml
+++ b/.github/workflows/cla.yml
@@ -5,8 +5,11 @@ on:
     types: [created]
   pull_request_target:
     types: [opened, synchronize]
+    branches: [main]
   # Run in merge queue but skip the step (shows as passing check)
   merge_group:
+    branches: [main]
+  workflow_dispatch:
 
 # Explicitly set permissions for the workflow
 permissions:
@@ -16,11 +19,20 @@ permissions:
   statuses: write
 
 jobs:
+  # Job for merge queue - always passes since CLA is checked at PR time
+  merge-queue-pass:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'merge_group' || github.event_name == 'workflow_dispatch'
+    steps:
+      - name: CLA already verified at PR time
+        run: echo "CLA check is performed on PRs, not in merge queue. Passing."
+
   cla-check:
     runs-on: ubuntu-latest
+    if: github.event_name != 'merge_group' && github.event_name != 'workflow_dispatch'
     steps:
       - name: "CLA Assistant"
-        if: github.event_name != 'merge_group' && ((github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target')
+        if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target'
         uses: contributor-assistant/github-action@v2.6.1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/claude-code-test.yml b/.github/workflows/claude-code-test.yml
index 84e888d0..7a113ff6 100644
--- a/.github/workflows/claude-code-test.yml
+++ b/.github/workflows/claude-code-test.yml
@@ -11,17 +11,31 @@ on:
         type: boolean
   # Run on all PRs (shows as check, but steps skip unless in merge queue)
   pull_request:
+    branches: [main]
   # Run in the merge queue to validate before merging
   merge_group:
+    branches: [main]
 
 # Ensure only one instance runs at a time per PR/branch
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
   cancel-in-progress: true
 
+# Minimal permissions for this workflow
+permissions:
+  contents: read
+
 jobs:
+  # Job for PRs - always passes, actual validation happens in merge queue
+  pr-check:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    steps:
+      - name: PR Check
+        run: echo "Claude Code integration tests will run in the merge queue"
+
   # Job 1: Validate command generation from fixtures (no API key needed)
-  # Runs on merge_group and workflow_dispatch, skipped on PRs (shows as passing check)
+  # Runs on merge_group and workflow_dispatch only
   validate-generation:
     runs-on: ubuntu-latest
     if: github.event_name == 'merge_group' || github.event_name == 'workflow_dispatch'
diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
index 5b3cfb74..a463b777 100644
--- a/.github/workflows/validate.yml
+++ b/.github/workflows/validate.yml
@@ -2,7 +2,14 @@ name: Validate
 
 on:
   pull_request:
+    branches: [main]
   merge_group:
+    branches: [main]
+  workflow_dispatch:
+
+# Minimal permissions for this workflow
+permissions:
+  contents: read
 
 jobs:
   tests: