diff --git a/manuscript.html b/manuscript.html
index 33ea0d58..c626cda5 100644
--- a/manuscript.html
+++ b/manuscript.html
@@ -6,7 +6,7 @@
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   <meta name="author" content="John Doe" />
   <meta name="author" content="Jane Roe" />
-  <meta name="dcterms.date" content="2024-07-31" />
+  <meta name="dcterms.date" content="2024-12-06" />
   <meta name="keywords" content="markdown, publishing, manubot" />
   <title>Manuscript Title</title>
   <style>
@@ -114,11 +114,11 @@
   <meta name="citation_title" content="Manuscript Title" />
   <meta property="og:title" content="Manuscript Title" />
   <meta property="twitter:title" content="Manuscript Title" />
-  <meta name="dc.date" content="2024-07-31" />
-  <meta name="citation_publication_date" content="2024-07-31" />
-  <meta property="article:published_time" content="2024-07-31" />
-  <meta name="dc.modified" content="2024-07-31T18:28:19+00:00" />
-  <meta property="article:modified_time" content="2024-07-31T18:28:19+00:00" />
+  <meta name="dc.date" content="2024-12-06" />
+  <meta name="citation_publication_date" content="2024-12-06" />
+  <meta property="article:published_time" content="2024-12-06" />
+  <meta name="dc.modified" content="2024-12-06T14:35:23+00:00" />
+  <meta property="article:modified_time" content="2024-12-06T14:35:23+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -139,9 +139,9 @@
   <meta name="citation_fulltext_html_url" content="https://manubot.github.io/rootstock/" />
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-  <meta name="manubot_html_url_versioned" content="https://manubot.github.io/rootstock/v/957ff8ebf04f1051aedb3fd17677e19ff2286b7a/" />
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+  <link rel="alternate" type="text/html" href="https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/" />
+  <meta name="manubot_html_url_versioned" content="https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/" />
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   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -165,10 +165,10 @@ <h1 class="title">Manuscript Title</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://manubot.github.io/rootstock/v/957ff8ebf04f1051aedb3fd17677e19ff2286b7a/">permalink</a>)
+(<a href="https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/">permalink</a>)
 was automatically generated
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-on July 31, 2024.
+from <a href="https://github.com/manubot/rootstock/tree/e5b62395d10a2b475c914726aafb510e41ce9015">manubot/rootstock@e5b6239</a>
+on December 6, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -425,7 +425,7 @@ <h2 id="tables">Tables</h2>
 </tbody>
 </table>
 </div>
-<div id="tbl:f1388a65-49f8-4227-8637-d6356b5468e9" class="tablenos">
+<div id="tbl:8cc392d1-5d34-4d7d-aed9-c0a8887c9b30" class="tablenos">
 <table id="tbl:">
 <caption><span>Table 3:</span> A table with merged cells using the <code>attributes</code> plugin.
 </caption>
diff --git a/manuscript.md b/manuscript.md
index 86ae7fb3..9561391f 100644
--- a/manuscript.md
+++ b/manuscript.md
@@ -5,7 +5,7 @@ keywords:
 - publishing
 - manubot
 lang: en-US
-date-meta: '2024-07-31'
+date-meta: '2024-12-06'
 author-meta:
 - John Doe
 - Jane Roe
@@ -20,11 +20,11 @@ header-includes: |
   <meta name="citation_title" content="Manuscript Title" />
   <meta property="og:title" content="Manuscript Title" />
   <meta property="twitter:title" content="Manuscript Title" />
-  <meta name="dc.date" content="2024-07-31" />
-  <meta name="citation_publication_date" content="2024-07-31" />
-  <meta property="article:published_time" content="2024-07-31" />
-  <meta name="dc.modified" content="2024-07-31T18:28:19+00:00" />
-  <meta property="article:modified_time" content="2024-07-31T18:28:19+00:00" />
+  <meta name="dc.date" content="2024-12-06" />
+  <meta name="citation_publication_date" content="2024-12-06" />
+  <meta property="article:published_time" content="2024-12-06" />
+  <meta name="dc.modified" content="2024-12-06T14:35:23+00:00" />
+  <meta property="article:modified_time" content="2024-12-06T14:35:23+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -45,9 +45,9 @@ header-includes: |
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+  <link rel="alternate" type="text/html" href="https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/" />
+  <meta name="manubot_html_url_versioned" content="https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/" />
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@@ -69,10 +69,10 @@ manubot-clear-requests-cache: false
 
 <small><em>
 This manuscript
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+([permalink](https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/))
 was automatically generated
-from [manubot/rootstock@957ff8e](https://github.com/manubot/rootstock/tree/957ff8ebf04f1051aedb3fd17677e19ff2286b7a)
-on July 31, 2024.
+from [manubot/rootstock@e5b6239](https://github.com/manubot/rootstock/tree/e5b62395d10a2b475c914726aafb510e41ce9015)
+on December 6, 2024.
 </em></small>
 
 
diff --git a/manuscript.pdf b/manuscript.pdf
index 7cbe113d..884e099a 100644
Binary files a/manuscript.pdf and b/manuscript.pdf differ
diff --git a/references.json b/references.json
index a5be47d3..d915973a 100644
--- a/references.json
+++ b/references.json
@@ -323,8 +323,8 @@
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         [
           2024,
-          7,
-          30
+          12,
+          6
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       ]
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@@ -433,8 +433,8 @@
       "date-parts": [
         [
           "2024",
-          7,
-          31
+          12,
+          6
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     },
diff --git a/variables.json b/variables.json
index a6a19365..a1783bd6 100644
--- a/variables.json
+++ b/variables.json
@@ -7,12 +7,12 @@
       "manubot"
     ],
     "lang": "en-US",
-    "date-meta": "2024-07-31",
+    "date-meta": "2024-12-06",
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       "Jane Roe"
     ],
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+    "header-includes": "<!--\nManubot generated metadata rendered from header-includes-template.html.\nSuggest improvements at https://github.com/manubot/manubot/blob/main/manubot/process/header-includes-template.html\n-->\n<meta name=\"dc.format\" content=\"text/html\" />\n<meta property=\"og:type\" content=\"article\" />\n<meta name=\"dc.title\" content=\"Manuscript Title\" />\n<meta name=\"citation_title\" content=\"Manuscript Title\" />\n<meta property=\"og:title\" content=\"Manuscript Title\" />\n<meta property=\"twitter:title\" content=\"Manuscript Title\" />\n<meta name=\"dc.date\" content=\"2024-12-06\" />\n<meta name=\"citation_publication_date\" content=\"2024-12-06\" />\n<meta property=\"article:published_time\" content=\"2024-12-06\" />\n<meta name=\"dc.modified\" content=\"2024-12-06T14:35:23+00:00\" />\n<meta property=\"article:modified_time\" content=\"2024-12-06T14:35:23+00:00\" />\n<meta name=\"dc.language\" content=\"en-US\" />\n<meta name=\"citation_language\" content=\"en-US\" />\n<meta name=\"dc.relation.ispartof\" content=\"Manubot\" />\n<meta name=\"dc.publisher\" content=\"Manubot\" />\n<meta name=\"citation_journal_title\" content=\"Manubot\" />\n<meta name=\"citation_technical_report_institution\" content=\"Manubot\" />\n<meta name=\"citation_author\" content=\"John Doe\" />\n<meta name=\"citation_author_institution\" content=\"Department of Something, University of Whatever\" />\n<meta name=\"citation_author_orcid\" content=\"XXXX-XXXX-XXXX-XXXX\" />\n<meta name=\"twitter:creator\" content=\"@johndoe\" />\n<meta name=\"citation_author\" content=\"Jane Roe\" />\n<meta name=\"citation_author_institution\" content=\"Department of Something, University of Whatever\" />\n<meta name=\"citation_author_institution\" content=\"Department of Whatever, University of Something\" />\n<meta name=\"citation_author_orcid\" content=\"XXXX-XXXX-XXXX-XXXX\" />\n<link rel=\"canonical\" href=\"https://manubot.github.io/rootstock/\" />\n<meta property=\"og:url\" content=\"https://manubot.github.io/rootstock/\" />\n<meta property=\"twitter:url\" content=\"https://manubot.github.io/rootstock/\" />\n<meta name=\"citation_fulltext_html_url\" content=\"https://manubot.github.io/rootstock/\" />\n<meta name=\"citation_pdf_url\" content=\"https://manubot.github.io/rootstock/manuscript.pdf\" />\n<link rel=\"alternate\" type=\"application/pdf\" href=\"https://manubot.github.io/rootstock/manuscript.pdf\" />\n<link rel=\"alternate\" type=\"text/html\" href=\"https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/\" />\n<meta name=\"manubot_html_url_versioned\" content=\"https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/\" />\n<meta name=\"manubot_pdf_url_versioned\" content=\"https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/manuscript.pdf\" />\n<meta property=\"og:type\" content=\"article\" />\n<meta property=\"twitter:card\" content=\"summary_large_image\" />\n<link rel=\"icon\" type=\"image/png\" sizes=\"192x192\" href=\"https://manubot.org/favicon-192x192.png\" />\n<link rel=\"mask-icon\" href=\"https://manubot.org/safari-pinned-tab.svg\" color=\"#ad1457\" />\n<meta name=\"theme-color\" content=\"#ad1457\" />\n<!-- end Manubot generated metadata -->\n",
     "bibliography": [
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@@ -22,10 +22,10 @@
     "manubot-clear-requests-cache": false
   },
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-    "date_long": "July 31, 2024",
-    "generated": "2024-07-31T18:28:19+00:00",
-    "generated_date_long": "July 31, 2024",
+    "date": "2024-12-06",
+    "date_long": "December 6, 2024",
+    "generated": "2024-12-06T14:35:23+00:00",
+    "generated_date_long": "December 6, 2024",
     "randomize_author_order": false,
     "authors": [
       {
@@ -79,17 +79,17 @@
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-      "triggering_commit": "957ff8ebf04f1051aedb3fd17677e19ff2286b7a",
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-      "job_url": "https://github.com/manubot/rootstock/actions/runs/10185651162"
+      "commit": "e5b62395d10a2b475c914726aafb510e41ce9015",
+      "triggering_commit": "e5b62395d10a2b475c914726aafb510e41ce9015",
+      "build_url": "https://github.com/manubot/rootstock/commit/e5b62395d10a2b475c914726aafb510e41ce9015/checks",
+      "job_url": "https://github.com/manubot/rootstock/actions/runs/12200632500"
     },
     "html_url": "https://manubot.github.io/rootstock/",
     "pdf_url": "https://manubot.github.io/rootstock/manuscript.pdf",
-    "html_url_versioned": "https://manubot.github.io/rootstock/v/957ff8ebf04f1051aedb3fd17677e19ff2286b7a/",
-    "pdf_url_versioned": "https://manubot.github.io/rootstock/v/957ff8ebf04f1051aedb3fd17677e19ff2286b7a/manuscript.pdf",
+    "html_url_versioned": "https://manubot.github.io/rootstock/v/e5b62395d10a2b475c914726aafb510e41ce9015/",
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     "manubot_version": "0.6.1",
-    "rootstock_commit": "957ff8ebf04f1051aedb3fd17677e19ff2286b7a",
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