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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-805e65de
+d9641f49
diff --git a/01-data-sources.html b/01-data-sources.html
@@ -2,12 +2,12 @@
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+<meta name="generator" content="quarto-1.5.52">
 
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-<title>Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook - 1&nbsp; Data sources: notes, contact information, and links</title>
+<title>1&nbsp; Data sources: notes, contact information, and links – Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook</title>
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         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-data-sources.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Data sources: notes, contact information, and links</span></a></li></ol></nav>
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+        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
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-      <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
+      <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
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@@ -153,9 +153,9 @@
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-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true">
  <span class="menu-text">Appendices</span></a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
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@@ -453,18 +453,7 @@ <h3 data-number="1.7.4" class="anchored" data-anchor-id="discard-rates-and-lengt
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@@ -496,15 +485,37 @@ <h3 data-number="1.7.4" class="anchored" data-anchor-id="discard-rates-and-lengt
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+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
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diff --git a/02-model-choices.html b/02-model-choices.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.52">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook - 2&nbsp; Modeling choices, notes and best practices</title>
+<title>2&nbsp; Modeling choices, notes and best practices – Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -107,13 +107,13 @@
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         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./02-model-choices.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Modeling choices, notes and best practices</span></a></li></ol></nav>
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+      <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
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@@ -182,9 +182,9 @@
 </li>
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       <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true">
  <span class="menu-text">Appendices</span></a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
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@@ -444,18 +444,7 @@ <h2 data-number="2.9" class="anchored" data-anchor-id="rockfish-steepness-profil
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@@ -487,15 +476,37 @@ <h2 data-number="2.9" class="anchored" data-anchor-id="rockfish-steepness-profil
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+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
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     var mailtoRegex = new RegExp(/^mailto:/);
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+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
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diff --git a/03-stock-synthesis.html b/03-stock-synthesis.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.52">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook - 3&nbsp; Running Stock Synthesis</title>
+<title>3&nbsp; Running Stock Synthesis – Unofficial NWFSC and SWFSC Groundfish Stock Assessment Handbook</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
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         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./03-stock-synthesis.html"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Running Stock Synthesis</span></a></li></ol></nav>
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       </button>
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@@ -153,9 +153,9 @@
 </li>
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       <div class="sidebar-item-container"> 
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+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true">
  <span class="menu-text">Appendices</span></a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
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@@ -272,18 +272,7 @@ <h2 data-number="3.2" class="anchored" data-anchor-id="model-tuning"><span class
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@@ -315,15 +304,37 @@ <h2 data-number="3.2" class="anchored" data-anchor-id="model-tuning"><span class
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+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
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