Fixed Code and CLI blocks

.obsidian/workspace.json

@@ -4,17 +4,21 @@
     "type": "split",
     "children": [
       {
-        "id": "63d80c6eb3872afa",
+        "id": "ae41ba9882c0a3d6",
         "type": "tabs",
         "children": [
           {
-            "id": "dc8c249564ffac56",
+            "id": "01161538f53367e8",
             "type": "leaf",
             "state": {
-              "type": "empty",
+              "type": "markdown",
-              "state": {},
+              "state": {
+                "file": "chapters/01_Getting_Started.md",
+                "mode": "source",
+                "source": false
+              },
               "icon": "lucide-file",
-              "title": "New tab"
+              "title": "01_Getting_Started"
             }
           }
         ]
@@ -264,26 +268,26 @@
       "obsidian-kanban:Create new board": false
     }
   },
-  "active": "dc8c249564ffac56",
+  "active": "01161538f53367e8",
   "lastOpenFiles": [
-    "conf/sedK5OZdk",
+    "conf/sedO6HWQd",
-    "conf/sed0lodyQ",
+    "conf/sedLQxQGf",
-    "conf/sedVrX4GJ",
+    "conf/sedIsN7C4",
-    "templates/odt.yaml",
+    "conf/sed8HHrHm",
-    "templates/frontmatter-docx.md",
+    "conf/sed0agSpY",
-    "templates/docx.yaml",
+    "conf/sed9gY2gw",
-    "scripts/new-project.sh",
+    "conf/seddo6XG6",
+    "conf/sedyheY4U",
+    "conf/seduL1p1z",
+    "conf/sedltGqhZ",
+    "conf/sedv2m0sa",
     "chapters/01_Getting_Started.md",
+    "templates/frontmatter-docx.md",
     "chapters/00_Introduction.md",
-    "conf/sedBC8U5P",
     "chapters/AppendixB.md",
     "chapters/03_Features.md",
     "chapters/02_Usage.md",
     "chapters/02_Features.md",
-    "conf/frontmatter.tex",
-    "conf/sed7Vpnn0",
-    "conf/latex.yaml",
-    "conf/sedOEGv7F",
     "chapters/Preface.md",
     "chapters/Index.md",
     "chapters/Glossary.md",

build/html/basic-book-builder.html

@@ -24,6 +24,71 @@
       vertical-align: middle;
     }
     .display.math{display: block; text-align: center; margin: 0.5rem auto;}
+    /* CSS for syntax highlighting */
+    html { -webkit-text-size-adjust: 100%; }
+    pre > code.sourceCode { white-space: pre; position: relative; }
+    pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+    pre > code.sourceCode > span:empty { height: 1.2em; }
+    .sourceCode { overflow: visible; }
+    code.sourceCode > span { color: inherit; text-decoration: inherit; }
+    div.sourceCode { margin: 1em 0; }
+    pre.sourceCode { margin: 0; }
+    @media screen {
+    div.sourceCode { overflow: auto; }
+    }
+    @media print {
+    pre > code.sourceCode { white-space: pre-wrap; }
+    pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+    }
+    pre.numberSource code
+      { counter-reset: source-line 0; }
+    pre.numberSource code > span
+      { position: relative; left: -4em; counter-increment: source-line; }
+    pre.numberSource code > span > a:first-child::before
+      { content: counter(source-line);
+        position: relative; left: -1em; text-align: right; vertical-align: baseline;
+        border: none; display: inline-block;
+        -webkit-touch-callout: none; -webkit-user-select: none;
+        -khtml-user-select: none; -moz-user-select: none;
+        -ms-user-select: none; user-select: none;
+        padding: 0 4px; width: 4em;
+        color: #aaaaaa;
+      }
+    pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
+    div.sourceCode
+      {   }
+    @media screen {
+    pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+    }
+    code span.al { color: #ff0000; font-weight: bold; } /* Alert */
+    code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
+    code span.at { color: #7d9029; } /* Attribute */
+    code span.bn { color: #40a070; } /* BaseN */
+    code span.bu { color: #008000; } /* BuiltIn */
+    code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
+    code span.ch { color: #4070a0; } /* Char */
+    code span.cn { color: #880000; } /* Constant */
+    code span.co { color: #60a0b0; font-style: italic; } /* Comment */
+    code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
+    code span.do { color: #ba2121; font-style: italic; } /* Documentation */
+    code span.dt { color: #902000; } /* DataType */
+    code span.dv { color: #40a070; } /* DecVal */
+    code span.er { color: #ff0000; font-weight: bold; } /* Error */
+    code span.ex { } /* Extension */
+    code span.fl { color: #40a070; } /* Float */
+    code span.fu { color: #06287e; } /* Function */
+    code span.im { color: #008000; font-weight: bold; } /* Import */
+    code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
+    code span.kw { color: #007020; font-weight: bold; } /* Keyword */
+    code span.op { color: #666666; } /* Operator */
+    code span.ot { color: #007020; } /* Other */
+    code span.pp { color: #bc7a00; } /* Preprocessor */
+    code span.sc { color: #4070a0; } /* SpecialChar */
+    code span.ss { color: #bb6688; } /* SpecialString */
+    code span.st { color: #4070a0; } /* String */
+    code span.va { color: #19177c; } /* Variable */
+    code span.vs { color: #4070a0; } /* VerbatimString */
+    code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
     /* CSS for citations */
     div.csl-bib-body { }
     div.csl-entry {
@@ -51,7 +116,7 @@
 
   <!-- Title Page -->
   <h1 class="titlepage" style="margin-top:3em; font-size:2.4em; text-align:center;">Basic Book Builder</h1>
-  <h2 style="text-align:center; font-weight:normal;">A Pandoc template for building books and articles</h2>
+  <h2 style="text-align:center; font-weight:normal;">A Pandoc template for building books, documents and articles</h2>
 
   <div style="text-align:center; margin:2em 0;">
     <img src="lib/img/UAF-ACEP.png" alt="Cover illustration" style="max-width:350px;">
@@ -64,13 +129,15 @@
   <div style="text-align:left; margin-top:5em;">
 
     <h2>Basic Book Builder</h2>
-    <i>A Pandoc template for building books and articles</i>
+    <i>A Pandoc template for building books, documents and articles</i>
 
     <table style="margin-top:2em; width:50%; border-collapse:collapse;">
       <tbody>
         <tr><td style="font-weight:bold;">Author</td><td>John Haverlack</td></tr>
         <tr><td style="font-weight:bold;">Version</td><td>1.1.0</td></tr>
         <tr><td style="font-weight:bold;">Date</td><td>2026-02-04</td></tr>
+        <tr><td style="font-weight:bold;">Affiliation</td><td>Alaska Center for Energy and Power</td></tr>
+        <tr><td style="font-weight:bold;">Institution</td><td>University of Alaska Fairbanks</td></tr>
         <tr><td style="font-weight:bold;">ISBN:</td><td>UNSPECIFIED</td></tr>
         <tr><td style="font-weight:bold;">DOI:</td><td>UNSPECIFIED</td></tr>
         <tr><td style="font-weight:bold;">Maturity</td><td>BETA</td></tr>
@@ -128,243 +195,207 @@ window.MathJax = {
 <nav id="TOC" role="doc-toc">
 <h2 id="toc-title">Contents</h2>
 <ul>
-<li><a href="#preface" id="toc-preface">Preface</a></li>
 <li><a href="#introduction" id="toc-introduction">Introduction</a></li>
 <li><a href="#getting-started" id="toc-getting-started">Getting
 Started</a>
 <ul>
-<li><a href="#installing-pre-requisites"
+<li><a href="#cloning-the-basic-book-builder"
-id="toc-installing-pre-requisites">Installing Pre-Requisites</a>
+id="toc-cloning-the-basic-book-builder">Cloning the Basic Book
-<ul>
+Builder</a></li>
-<li><a href="#required" id="toc-required">Required</a></li>
+<li><a href="#setting-up-build-environment"
-<li><a href="#optional" id="toc-optional">Optional</a></li>
+id="toc-setting-up-build-environment">Setting Up Build
-</ul></li>
+Environment</a></li>
-<li><a href="#editing-the-configuration"
-id="toc-editing-the-configuration">Editing the Configuration</a></li>
-</ul></li>
-<li><a href="#editing-the-book" id="toc-editing-the-book">Editing the
-Book</a>
-<ul>
-<li><a href="#configuration"
-id="toc-configuration">Configuration</a></li>
-<li><a href="#frontmatter-config"
-id="toc-frontmatter-config">FrontMatter Config</a></li>
-<li><a href="#editing-the-content" id="toc-editing-the-content">Editing
-the Content</a>
-<ul>
-<li><a href="#citations" id="toc-citations">Citations</a></li>
-</ul></li>
-<li><a href="#usage-building-the-book"
-id="toc-usage-building-the-book">Usage: Building the Book</a></li>
 </ul></li>
 <li><a href="#glossary" id="toc-glossary">Glossary</a></li>
 <li><a href="#bibliography" id="toc-bibliography">Bibliography</a></li>
 </ul>
 </nav>
-<h1 class="unnumbered" id="preface">Preface</h1>
-<p>Preface to the Book…</p>
 <h1 id="introduction">Introduction</h1>
-<p>This is a basic book (or article) builder template based on a Pandoc
+<p>This is a basic book (or article / document) builder template based
-build process in conjunction with a number of other tools to generate
+on a Pandoc<span class="citation" data-cites="PandocIndex">(<a
-PDF, ODT, HTML, LaTex, Markdown, and Epub book output formats from
+href="#ref-PandocIndex" role="doc-biblioref"><em>Pandoc - Index</em>,
-Markdown source content , which can optionally be edited as an Obsidian
+n.d.</a>)</span> build process in conjunction with a number of other
-vault.</p>
+tools to generate PDF, HTML, LaTex, Markdown, ODT, DOCX, and Epub book
-<p>This book builder template has been curated by John Haverlack.<span
+output formats from a single set Markdown source content , which can
+optionally be edited as an Obsidian vault.</p>
+<p>This <strong>basic book builder</strong><span class="citation"
+data-cites="JehaverlackBasicbookbuilderPandoca">(<a
+href="#ref-JehaverlackBasicbookbuilderPandoca"
+role="doc-biblioref"><em>Jehaverlack/Basic-Book-Builder</em>,
+n.d.</a>)</span> template has been curated by John Haverlack.<span
 class="citation" data-cites="JohnHaverlackACEP">(<a
 href="#ref-JohnHaverlackACEP" role="doc-biblioref"><em>John
 <span>Haverlack</span> <span>ACEP</span></em>, n.d.</a>)</span></p>
 <h1 id="getting-started">Getting Started</h1>
-<h2 id="installing-pre-requisites">Installing Pre-Requisites</h2>
+<h2 id="cloning-the-basic-book-builder">Cloning the Basic Book
-<p>For Debian / ZorinOS and likely Ubuntu based systems.</p>
+Builder</h2>
+<div class="callout-cli">
+<p><strong>Cloning the repository</strong></p>
+<div class="sourceCode" id="cb1"><pre
+class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://github.com/jehaverlack/basic-book-builder.git</span></code></pre></div>
+</div>
+<div class="callout-cli">
+<p><strong>Navigate to the repo directory</strong></p>
+<pre><code>cd basic-book-builder</code></pre>
+</div>
+<h2 id="setting-up-build-environment">Setting Up Build Environment</h2>
 <div class="callout-caution">
-<p><strong>TODO</strong></p>
+<p><strong>Debian Based Linux</strong></p>
-<p> It would be nice to roll a setup script to take care of this.</p>
+<p> This script only support Debian based linux system (Debian, Ubunutu,
+Zorin, etc) This script has not been widely tested across platforms</p>
 </div>
-<h3 id="required">Required</h3>
+<div class="callout-cli">
-<h4 id="pandoc">Pandoc</h4>
+<p><strong>Setup Build Environment</strong></p>
-<ul>
+<div class="sourceCode" id="cb3"><pre
-<li>https://pandoc.org/</li>
+class="sourceCode bash"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">./scripts/setup-linux-deb.sh</span></span></code></pre></div>
-<li><a
-href="https://github.com/jgm/pandoc/releases/tag/3.8.2.1">Download</a></li>
-</ul>
-<blockquote>
-<p><code>sudo apt install https://github.com/jgm/pandoc/releases/download/3.8.2.1/pandoc-3.8.2.1-1-amd64.deb</code></p>
-</blockquote>
-<h4 id="code-editor">Code Editor</h4>
-<div class="callout-established">
-<p><strong>Code Editor</strong></p>
-<p> <a href="https://vscodium.com/">VSCodium</a> is recommend for
-privacy (telemetry/tracking) reasons - https://vscodium.com/</p>
 </div>
-<p>But any text editor will work. #### make</p>
+<p>For more information on setting up the build environment for your
-<pre><code>sudo apt install make</code></pre>
+system see Appendix A.</p>
-<h4 id="jq-and-yq">jq and yq</h4>
-<pre><code>sudo apt install jq yq</code></pre>
-<h4 id="texlive">texlive</h4>
-<blockquote>
-<p><code>sudo apt install texlive texlive-xetex texlive-latex-extra texlive-fonts-recommended texlive-fonts-extra</code></p>
-</blockquote>
-<h4 id="mathjax">MathJax</h4>
-<ul>
-<li>https://www.mathjax.org/</li>
-</ul>
-<pre><code>wget https://registry.npmjs.org/mathjax/-/mathjax-3.2.2.tgz
-tar xzf mathjax-3.2.2.tgz
-mv package/es5/* lib/mathjax
-rm -rf package mathjax-3.2.2.tgz</code></pre>
-<div class="callout-caution">
-<p><strong>TODO</strong></p>
-<p> This need to be rolled into a setup script.</p>
-</div>
-<h3 id="optional">Optional</h3>
-<p>The following are not strictly requires to use this book builder
-template.</p>
-<h4 id="obsidian">Obsidian</h4>
-<div class="callout-established">
-<p><strong>Highly Recommended</strong></p>
-<p> Editing book chapter content in Obsidian is a very productive means
-for editing Markdown source content.</p>
-</div>
-<ul>
-<li>https://obsidian.md/</li>
-<li><a
-href="https://github.com/obsidianmd/obsidian-releases/releases/download/v1.9.14/obsidian_1.9.14_amd64.deb">Deb
-Package</a></li>
-</ul>
-<pre><code>sudo apt install https://github.com/obsidianmd/obsidian-releases/releases/download/v1.9.14/obsidian_1.9.14_amd64.deb</code></pre>
-<h4 id="zotero">Zotero</h4>
-<div class="callout-established">
-<p><strong>Highly Recommended</strong></p>
-<p> If you need to managed citations and references, Zotero integration
-is highly recommended.</p>
-</div>
-<ul>
-<li>https://www.zotero.org/</li>
-</ul>
-<pre><code>sudo cp ./scripts/deps/zotero.list /etc/apt/sources.list.d/</code></pre>
-<pre><code>sudo apt update</code></pre>
-<pre><code>sudo apt install zotero</code></pre>
-<h5 id="better-bibtex-for-zotero">Better BibTex for Zotero</h5>
-<p>Install the Better BibTex Plugin for Zotero - Zotero &gt; Tool &gt;
-Plugins</p>
-<h5 id="export-citations.bib">Export citations.bib</h5>
-<ul>
-<li>Zotero &gt; File &gt; Export Library &gt; Format: Better BibTeX</li>
-<li><label><input type="checkbox" />Keep Updated</label></li>
-<li><label><input type="checkbox" />Save to:
-~/Documents/Lib/zotero.bib</label></li>
-<li><label><input type="checkbox" />Symlink your
-~/Documents/Lib/Citations.bib to
-basic-book-builder/lib/zotero.bib</label></li>
-</ul>
-<h5 id="zotero-connector-browser-plugin">Zotero Connector Browser
-Plugin</h5>
-<ul>
-<li>https://chromewebstore.google.com/detail/zotero-connector/ekhagklcjbdpajgpjgmbionohlpdbjgc</li>
-</ul>
-<p>Provides you the ability to auto add Web resources to your Zotero
-citation database.</p>
-<h4 id="lmodern">lmodern</h4>
-<pre><code>sudo apt install lmodern</code></pre>
-<h4 id="epubcheck">epubcheck</h4>
-<pre><code>sudo apt install epubcheck</code></pre>
-<h4 id="foliate">foliate</h4>
-<p>An EPub Reader</p>
-<ul>
-<li>https://johnfactotum.github.io/foliate/</li>
-</ul>
-<pre><code>sudo apt install https://github.com/johnfactotum/foliate/releases/download/2.6.4/com.github.johnfactotum.foliate_2.6.4_all.deb</code></pre>
-<h4 id="calibre">calibre</h4>
-<p>An EPub Reader</p>
-<ul>
-<li>https://calibre-ebook.com</li>
-</ul>
-<pre><code>sudo apt install calibre</code></pre>
-<h2 id="editing-the-configuration">Editing the Configuration</h2>
-<h1 id="editing-the-book">Editing the Book</h1>
-<h3 id="configuration">Configuration</h3>
-<p>There are a number of other config files for each format:</p>
-<pre><code>conf/
-├── epub-metadata.xml
-├── epub_template.html
-├── epub.yaml
-├── frontmatter_epub.md
-├── frontmatter_epub.xhtml
-├── frontmatter.html
-├── frontmatter.tex
-├── header.tex
-├── html.yaml
-├── latex.yaml
-├── markdown.yaml
-├── metadata.yaml
-├── pandoc.yaml
-├── pdf.yaml
-├── style.css
-└── style_epub.css
-</code></pre>
-<h4 id="main-config-files">Main Config Files</h4>
-<ul>
-<li>metadata.yaml - Set Title, etc</li>
-<li>pandoc.yaml - Main Pandoc Config #### Per format Configs</li>
-<li><code>pdf.yaml</code></li>
-<li><code>html.yaml</code></li>
-<li><code>latex.yaml</code></li>
-<li><code>epub.yaml</code></li>
-</ul>
-<h3 id="frontmatter-config">FrontMatter Config</h3>
-<p>There are 2 Version of the FrontMatter for PDF, and HTML bases
-formats that set the Title, Author, Verizon, Copyright, etc…</p>
-<ul>
-<li><code>frontmatter.tex</code></li>
-<li><code>frontmatter.html</code></li>
-<li><code>frontmatter_epub.*</code> - Work in Progress</li>
-</ul>
-<blockquote>
-<p>There is probably a better way to do this.</p>
-</blockquote>
-<h2 id="editing-the-content">Editing the Content</h2>
-<p>To edit the book open the <code>basic-book-builder</code> directory
-as an Obsidian Vault.</p>
-<ul>
-<li>Edit the Markdown content in the <code>chapters</code>
-directory.</li>
-</ul>
-<h3 id="citations">Citations</h3>
-<blockquote>
-<p>Note: the Zotero database needs configured to export automatically to
-<code>lib/citations.bib</code></p>
-</blockquote>
-<p>To insert a Zotero Citation - Ensure the Zotero App and DB are
-running on you system. - Alt + I (to insert citation) - Search for and
-select citation reference</p>
-<h2 id="usage-building-the-book">Usage: Building the Book</h2>
-<h4 id="pdf">PDF</h4>
-<pre><code>make pdf</code></pre>
-<h4 id="html">HTML</h4>
-<pre><code>make html</code></pre>
-<h4 id="latex">LaTex</h4>
-<pre><code>make latex</code></pre>
-<h4 id="markdown">Markdown</h4>
-<pre><code>make markdown</code></pre>
-<h4 id="epub">EPub</h4>
-<blockquote>
-<p>Note: This ePub configuration still needs tuning.</p>
-</blockquote>
-<pre><code>make epub</code></pre>
-<p>Appendix A</p>
-<p>First Appendix</p>
 <h1 class="unnumbered" id="glossary">Glossary</h1>
-<ul>
+<table>
-<li><strong>AI</strong> - Artificial Intelligence</li>
+<colgroup>
-<li></li>
+<col style="width: 17%" />
-</ul>
+<col style="width: 82%" />
+</colgroup>
+<thead>
+<tr>
+<th>Term</th>
+<th>Description</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><strong>AST (Abstract Syntax Tree)</strong></td>
+<td>Pandoc’s internal structured representation of a document. Lua
+filters operate on the AST before rendering to a target format.</td>
+</tr>
+<tr>
+<td><strong>Bibliography</strong></td>
+<td>A <code>.bib</code> file (e.g., Zotero export) used by Pandoc with
+<code>citeproc</code> to generate formatted citations and reference
+lists.</td>
+</tr>
+<tr>
+<td><strong>Callout</strong></td>
+<td>A styled block (e.g., <code>[!warning]</code>) transformed by Lua
+filters into format-specific output such as LaTeX environments or HTML
+<code>&lt;div&gt;</code> elements.</td>
+</tr>
+<tr>
+<td><strong>Defaults File (YAML)</strong></td>
+<td>A Pandoc configuration file defining output format, filters,
+metadata, and rendering options (e.g., <code>pdf.yaml</code>,
+<code>html.yaml</code>).</td>
+</tr>
+<tr>
+<td><strong>DOCX</strong></td>
+<td>Microsoft Word document format generated by Pandoc; styling is
+controlled via a <code>reference.docx</code> file.</td>
+</tr>
+<tr>
+<td><strong>Filter (Lua)</strong></td>
+<td>A script that modifies Pandoc’s AST before rendering. Used in this
+workflow for callouts and other structural transformations.</td>
+</tr>
+<tr>
+<td><strong>Frontmatter</strong></td>
+<td>Format-specific content inserted before the main body (e.g.,
+<code>frontmatter.tex</code>, <code>frontmatter.html</code>,
+<code>frontmatter-docx.md</code>).</td>
+</tr>
+<tr>
+<td><strong>HTML</strong></td>
+<td>Web output format generated by Pandoc, typically styled via CSS and
+supporting interactive features.</td>
+</tr>
+<tr>
+<td><strong>LaTeX</strong></td>
+<td>Typesetting system used for high-quality PDF generation via XeLaTeX
+in this workflow.</td>
+</tr>
+<tr>
+<td><strong>Lua Filter</strong></td>
+<td>A lightweight scripting extension used by Pandoc to customize
+document transformations programmatically.</td>
+</tr>
+<tr>
+<td><strong>Makefile</strong></td>
+<td>Automation script orchestrating the build pipeline for PDF, HTML,
+DOCX, ODT, and Markdown outputs.</td>
+</tr>
+<tr>
+<td><strong>Markdown</strong></td>
+<td>Plain-text markup language serving as the source format for all
+outputs in the workflow.</td>
+</tr>
+<tr>
+<td><strong>Metadata</strong></td>
+<td>Key–value pairs (e.g., <code>metadata.yaml</code>) defining title,
+author, license, version, and other document variables.</td>
+</tr>
+<tr>
+<td><strong>ODT</strong></td>
+<td>OpenDocument Text format used by LibreOffice; similar to DOCX but
+open-standard.</td>
+</tr>
+<tr>
+<td><strong>Pandoc</strong></td>
+<td>Universal document converter used to transform Markdown into PDF,
+HTML, DOCX, ODT, EPUB, and more.</td>
+</tr>
+<tr>
+<td><strong>PDF</strong></td>
+<td>Portable Document Format output produced via Pandoc + XeLaTeX.</td>
+</tr>
+<tr>
+<td><strong>Reference Document</strong></td>
+<td>A DOCX or ODT file defining styles (fonts, headings, spacing) used
+when generating Word/LibreOffice outputs.</td>
+</tr>
+<tr>
+<td><strong>Resource Path</strong></td>
+<td>Directories Pandoc searches for images, diagrams, and other assets
+during rendering.</td>
+</tr>
+<tr>
+<td><strong>Template</strong></td>
+<td>A format-specific layout file (e.g., LaTeX template) used to control
+document structure beyond styling.</td>
+</tr>
+<tr>
+<td><strong>TOC (Table of Contents)</strong></td>
+<td>Automatically generated navigation structure controlled by
+<code>toc</code> and <code>toc-depth</code> options.</td>
+</tr>
+<tr>
+<td><strong>XeLaTeX</strong></td>
+<td>LaTeX engine used to generate PDFs with modern font support (via
+<code>fontspec</code>).</td>
+</tr>
+<tr>
+<td><strong>Zotero</strong></td>
+<td>Reference manager used to generate <code>.bib</code> files for
+citation processing with Pandoc.</td>
+</tr>
+</tbody>
+</table>
 <h1 class="unnumbered" id="bibliography">Bibliography</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
 role="list">
+<div id="ref-JehaverlackBasicbookbuilderPandoca" class="csl-entry"
+role="listitem">
+<em>Jehaverlack/Basic-Book-Builder: <span>A Pandoc</span> Workflow for
+Building <span>PDF</span>, <span>HTML</span>, <span>EPUB</span>, and
+<span>LaTeX</span> Book Format.</em> n.d.
+Https://github.com/jehaverlack/basic-book-builder.
+</div>
 <div id="ref-JohnHaverlackACEP" class="csl-entry" role="listitem">
 <em>John <span>Haverlack</span> <span>ACEP</span></em>. n.d.
 Https://www.uaf.edu/acep/about/our-team/john-haverlack.php.
 </div>
+<div id="ref-PandocIndex" class="csl-entry" role="listitem">
+<em>Pandoc - Index</em>. n.d. Https://pandoc.org/.
+</div>
 </div>
 </body>
 </html>

build/html/conf/style.css

@@ -89,7 +89,9 @@ ul, ol {
 .callout-speculative,
 .callout-caution,
 .callout-warning,
-.callout-danger {
+.callout-danger,
+.callout-code,
+.callout-cli {
   border-radius: 6px;
   padding: 5px;  /* internal padding */
   margin-top: 5px;     /* external spacing tightened */
@@ -104,7 +106,9 @@ ul, ol {
 .callout-speculative p:first-child strong,
 .callout-caution p:first-child strong,
 .callout-warning p:first-child strong,
-.callout-danger p:first-child strong {
+.callout-danger p:first-child strong,
+.callout-code p:first-child strong,
+.callout-cli p:first-child strong {
   display: block;
   font-family: "Libertinus Sans", sans-serif;
   font-weight: 600;
@@ -118,7 +122,9 @@ ul, ol {
 .callout-speculative p,
 .callout-caution p,
 .callout-warning p,
-.callout-danger p {
+.callout-danger p,
+.callout-code p,
+.callout-cli p {
   margin-top: 5px;
   margin-bottom: 5px;
   line-height: 1.45;  /* slightly condensed text spacing */
@@ -181,6 +187,23 @@ ul, ol {
   border-left-color: #d83b3a;
 }
 
+/* ------------------------------
+   Code / CLI Callouts
+   ------------------------------ */
+
+  .callout-code {
+  background: #f5f5f5;
+  border-left-color: #b4b4b4;
+}
+
+.callout-cli {
+  background: #f0f0f0;
+  border-left-color: #777;
+  font-family: "Noto Sans Mono", monospace;
+  font-size: 0.95em;
+}
+
+  
 /* ------------------------------
    Images (in body content)
    ------------------------------ */

build/html/lib/img/Revolving_circles.svg

@@ -1 +0,0 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 0 350 350"><path fill="#aaa" d="M0 0h350v350H0z"/><g transform="translate(175 175)"><circle r="3"/><g fill="none" stroke-linecap="square"><g id="a"><path stroke="#eee" d="m-8-106 4-12H9"/><path stroke="#777" d="m9-118-4 12H-8"/></g><use xlink:href="#a" transform="rotate(12)"/><use xlink:href="#a" transform="rotate(24)"/><use xlink:href="#a" transform="rotate(36)"/><use xlink:href="#a" transform="rotate(48)"/><use xlink:href="#a" transform="rotate(60)"/><use xlink:href="#a" transform="rotate(72)"/><use xlink:href="#a" transform="rotate(84)"/><use xlink:href="#a" transform="rotate(96)"/><use xlink:href="#a" transform="rotate(108)"/><use xlink:href="#a" transform="rotate(120)"/><use xlink:href="#a" transform="rotate(132)"/><use xlink:href="#a" transform="rotate(144)"/><use xlink:href="#a" transform="rotate(156)"/><use xlink:href="#a" transform="rotate(168)"/><use xlink:href="#a" transform="rotate(180)"/><use xlink:href="#a" transform="rotate(-12)"/><use xlink:href="#a" transform="rotate(-24)"/><use xlink:href="#a" transform="rotate(-36)"/><use xlink:href="#a" transform="rotate(-48)"/><use xlink:href="#a" transform="rotate(-60)"/><use xlink:href="#a" transform="rotate(-72)"/><use xlink:href="#a" transform="rotate(-84)"/><use xlink:href="#a" transform="rotate(-96)"/><use xlink:href="#a" transform="rotate(-108)"/><use xlink:href="#a" transform="rotate(-120)"/><use xlink:href="#a" transform="rotate(-132)"/><use xlink:href="#a" transform="rotate(-144)"/><use xlink:href="#a" transform="rotate(-156)"/><use xlink:href="#a" transform="rotate(-168)"/><g id="b"><path stroke="#eee" d="m10-135-4-12H-7"/><path stroke="#777" d="m-7-147 4 12h13"/></g><use xlink:href="#b" transform="rotate(10)"/><use xlink:href="#b" transform="rotate(20)"/><use xlink:href="#b" transform="rotate(30)"/><use xlink:href="#b" transform="rotate(40)"/><use xlink:href="#b" transform="rotate(50)"/><use xlink:href="#b" transform="rotate(60)"/><use xlink:href="#b" transform="rotate(70)"/><use xlink:href="#b" transform="rotate(80)"/><use xlink:href="#b" transform="rotate(90)"/><use xlink:href="#b" transform="rotate(100)"/><use xlink:href="#b" transform="rotate(110)"/><use xlink:href="#b" transform="rotate(120)"/><use xlink:href="#b" transform="rotate(130)"/><use xlink:href="#b" transform="rotate(140)"/><use xlink:href="#b" transform="rotate(150)"/><use xlink:href="#b" transform="rotate(160)"/><use xlink:href="#b" transform="rotate(170)"/><use xlink:href="#b" transform="rotate(180)"/><use xlink:href="#b" transform="rotate(-10)"/><use xlink:href="#b" transform="rotate(-20)"/><use xlink:href="#b" transform="rotate(-30)"/><use xlink:href="#b" transform="rotate(-40)"/><use xlink:href="#b" transform="rotate(-50)"/><use xlink:href="#b" transform="rotate(-60)"/><use xlink:href="#b" transform="rotate(-70)"/><use xlink:href="#b" transform="rotate(-80)"/><use xlink:href="#b" transform="rotate(-90)"/><use xlink:href="#b" transform="rotate(-100)"/><use xlink:href="#b" transform="rotate(-110)"/><use xlink:href="#b" transform="rotate(-120)"/><use xlink:href="#b" transform="rotate(-130)"/><use xlink:href="#b" transform="rotate(-140)"/><use xlink:href="#b" transform="rotate(-150)"/><use xlink:href="#b" transform="rotate(-160)"/><use xlink:href="#b" transform="rotate(-170)"/></g></g></svg>

build/latex/basic-book-builder.aux

@@ -33,16 +33,16 @@
 \gdef \LT@i {\LT@entry 
     {1}{86.68152pt}\LT@entry 
     {1}{383.07349pt}}
-\newlabel{glossary}{{2.2}{3}{Glossary}{chapter*.4}{}}
+\newlabel{glossary}{{2.2}{4}{Glossary}{chapter*.4}{}}
-\@writefile{toc}{\contentsline {chapter}{Glossary}{3}{chapter*.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Glossary}{4}{chapter*.4}\protected@file@percent }
-\@writefile{toc}{\contentsline {chapter}{Index}{5}{chapter*.5}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Index}{6}{chapter*.5}\protected@file@percent }
 \bibcite{ref-JehaverlackBasicbookbuilderPandoca}{\citeproctext }
 \bibcite{ref-JohnHaverlackACEP}{\citeproctext }
 \bibcite{ref-PandocIndex}{\citeproctext }
 \bibcite{ref-JehaverlackBasicbookbuilderPandoca}{\citeproctext }
 \bibcite{ref-JohnHaverlackACEP}{\citeproctext }
 \bibcite{ref-PandocIndex}{\citeproctext }
-\newlabel{bibliography}{{2.2}{7}{Bibliography}{chapter*.6}{}}
+\newlabel{bibliography}{{2.2}{8}{Bibliography}{chapter*.6}{}}
-\@writefile{toc}{\contentsline {chapter}{Bibliography}{7}{chapter*.6}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Bibliography}{8}{chapter*.6}\protected@file@percent }
-\newlabel{refs}{{2.2}{7}{Bibliography}{section*.7}{}}
+\newlabel{refs}{{2.2}{8}{Bibliography}{section*.7}{}}
-\gdef \@abspage@last{12}
+\gdef \@abspage@last{13}

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 \LTright=\skip54
 \LTpre=\skip55
 \LTpost=\skip56
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+\LTchunksize=\count292
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+\LT@head=\box55
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 Package: array 2022/09/04 v2.5g Tabular extension package (FMi)
 \col@sep=\dimen176
-\ar@mcellbox=\box61
+\ar@mcellbox=\box60
 \extrarowheight=\dimen177
 \NC@list=\toks25
 \extratabsurround=\skip57
 \backup@length=\skip58
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+\ar@cellbox=\box61
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 Package: calc 2017/05/25 v4.3 Infix arithmetic (KKT,FJ)
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 \calc@Bdimen=\dimen179
 \calc@Askip=\skip59
 \calc@Bskip=\skip60
 LaTeX Info: Redefining \setlength on input line 80.
 LaTeX Info: Redefining \addtolength on input line 81.
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 Package: footnotehyper 2021/08/13 v1.1e hyperref aware footnote.sty (JFB)
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 File: lstmisc.sty 2020/03/24 1.8d (Carsten Heinz)
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 Writing index file basic-book-builder.idx
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 LaTeX Info: Redefining \url on input line 4748.
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 Package: rerunfilecheck 2022-07-10 v1.10 Rerun checks for auxiliary files (HO)
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 *geometry* driver: auto-detecting
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 LaTeX Font Info:    Overwriting symbol font `operators' in version `normal'
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 Package fontspec Info: latinmodern-math scale = 1.243617846722112.
 
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-t line 303.
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-Package microtype Info: Applying patch `item' on input line 303.
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-Package microtype Info: Applying patch `toc' on input line 303.
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-Package microtype Info: Applying patch `eqnum' on input line 303.
+Package microtype Info: Applying patch `eqnum' on input line 294.
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+Package microtype Info: Applying patch `footnote' on input line 294.
 Package microtype Info: Character protrusion enabled (level 2).
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 Package microtype Info: No adjustment of tracking.
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 (microtype)             See the microtype manual for details.
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 LaTeX Font Info:    Trying to load font information for OML+lmm on input line 3
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 (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd
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 )
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+LaTeX Font Info:    Trying to load font information for U+msb on input line 329
 .
 
 (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd
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  [2]
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-\tf@toc=\write6
+\tf@toc=\write5
-\openout6 = `basic-book-builder.toc'.
+\openout5 = `basic-book-builder.toc'.
 
  [1
 
@@ -1761,51 +1752,57 @@ Chapter 1.
 ]
 Chapter 2.
 LaTeX Font Info:    Font shape `TU/NotoSansMono(0)/m/n' will be
-(Font)              scaled to size 12.0pt on input line 445.
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+
+Overfull \hbox (10.34296pt too wide) in paragraph at lines 434--434
+[]\TU/NotoSansMono(0)/m/n/12 git clone https://github.com/jehaverlack/basic-boo
+k-builder.git[] 
+ []
+
 [2
 
-]
+] [3]
-Underfull \hbox (badness 10000) in alignment at lines 488--496
+Underfull \hbox (badness 10000) in alignment at lines 479--487
 [] []
  []
 
 
-Underfull \hbox (badness 10000) in alignment at lines 496--498
+Underfull \hbox (badness 10000) in alignment at lines 487--489
 [] []
  []
 
 
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+Overfull \hbox (1.68248pt too wide) in paragraph at lines 493--493
 []|\TU/NotoSerif(0)/b/n/12 Bibliography|  
  []
 
 
-Underfull \hbox (badness 10000) in alignment at lines 498--550
+Underfull \hbox (badness 10000) in alignment at lines 489--541
 [] []
  []
 
-[3
+[4
 
 
-] [4] (./basic-book-builder.ind) [5
+] [5] (./basic-book-builder.ind) [6
 
-] [6
+] [7
 
 ]
-Underfull \hbox (badness 3977) in paragraph at lines 585--587
+Underfull \hbox (badness 3977) in paragraph at lines 576--578
 []\TU/NotoSerif(0)/m/it/12 John Haverlack | ACEP\TU/NotoSerif(0)/m/n/12 . n.d. 
 Https://www.uaf.edu/acep/about/our-team/john-
  []
 
 
-Underfull \hbox (badness 3977) in paragraph at lines 597--599
+Underfull \hbox (badness 3977) in paragraph at lines 588--590
 []\TU/NotoSerif(0)/m/it/12 John Haverlack | ACEP\TU/NotoSerif(0)/m/n/12 . n.d. 
 Https://www.uaf.edu/acep/about/our-team/john-
  []
 
-[7
+[8
 
-] [8
+] [9
 
 ] (./basic-book-builder.aux)
 
@@ -1813,12 +1810,12 @@ LaTeX Warning: There were multiply-defined labels.
 
  ) 
 Here is how much of TeX's memory you used:
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+ 745203 string characters out of 5850945
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-Output written on basic-book-builder.pdf (12 pages).
+Output written on basic-book-builder.pdf (13 pages).

build/latex/basic-book-builder.tex

@@ -42,44 +42,6 @@
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-\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
-\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{#1}}}
-\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
-\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.53,0.00,0.00}{#1}}
-\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{#1}}}
-\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{#1}}
-\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}}
-\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.73,0.13,0.13}{\textit{#1}}}
-\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{#1}}}
-\newcommand{\ExtensionTok}[1]{#1}
-\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{#1}}
-\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{#1}}
-\newcommand{\ImportTok}[1]{\textcolor[rgb]{0.00,0.50,0.00}{\textbf{#1}}}
-\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
-\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{#1}}}
-\newcommand{\NormalTok}[1]{#1}
-\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.40,0.40,0.40}{#1}}
-\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{#1}}
-\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.74,0.48,0.00}{#1}}
-\newcommand{\RegionMarkerTok}[1]{#1}
-\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
-\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.73,0.40,0.53}{#1}}
-\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
-\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.10,0.09,0.49}{#1}}
-\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{#1}}
-\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{#1}}}}
 \usepackage{longtable,booktabs,array}
 \newcounter{none} % for unnumbered tables
 \usepackage{calc} % for calculating minipage widths
@@ -158,6 +120,8 @@
 \usepackage{xcolor}
 \definecolor{speculativeback}{RGB}{247,232,255}  % #f7e8ff
 \definecolor{speculativeframe}{RGB}{139,43,226}  % #8b2be2
+\definecolor{lightgrayback}{RGB}{245,245,245}
+\definecolor{lightgrayframe}{RGB}{180,180,180}
 
 % --- Left-align all Pandoc tables ---
 \usepackage{longtable}
@@ -257,6 +221,33 @@
   after=\par\vspace{6pt}
 }
 
+
+% =========================================================
+% Code / CLI Boxes
+% =========================================================
+
+\newtcolorbox{codebox}[1][Code]{%
+  title=\ifstrempty{#1}{\blanktitle}{#1},
+  colback=lightgrayback,
+  colframe=lightgrayframe,
+  colbacktitle=lightgrayback!90!white,
+  fonttitle=\bfseries,
+  coltitle=black,
+  enhanced, sharp corners, breakable,
+  after=\par\vspace{6pt}
+}
+
+\newtcolorbox{clibox}[1][Command Line]{%
+  title=\ifstrempty{#1}{\blanktitle}{#1},
+  colback=lightgrayback,
+  colframe=lightgrayframe,
+  colbacktitle=lightgrayback!90!white,
+  fonttitle=\bfseries,
+  coltitle=black,
+  enhanced, sharp corners, breakable,
+  after=\par\vspace{6pt}
+}
+
 \usepackage{xurl}
 
 \usepackage{fancyhdr}
@@ -438,23 +429,26 @@ Haverlack.(\citeproc{ref-JohnHaverlackACEP}{\emph{John {Haverlack}
 \section{Cloning the Basic Book
 Builder}\label{cloning-the-basic-book-builder}
 
-\begin{quote}
+\begin{clibox}[Cloning the repository]
-{[}!cli{]} Cloning the repository
+\begin{verbatim}
+git clone https://github.com/jehaverlack/basic-book-builder.git
+\end{verbatim}
 
-\begin{Shaded}
+\end{clibox}
-\begin{Highlighting}[]
-\FunctionTok{git}\NormalTok{ clone https://github.com/jehaverlack/basic{-}book{-}builder.git}
-\end{Highlighting}
-\end{Shaded}
-\end{quote}
-
-\begin{quote}
-{[}!cli{]} Navigate to the repo directory
 
+\begin{clibox}[Navigate to the repo directory]
 \begin{verbatim}
 cd basic-book-builder
 \end{verbatim}
-\end{quote}
+
+\end{clibox}
+
+\begin{codebox}[Code Example]
+\begin{verbatim}
+if then else
+\end{verbatim}
+
+\end{codebox}
 
 \section{Setting Up Build
 Environment}\label{setting-up-build-environment}
@@ -464,15 +458,12 @@ This script only support Debian based linux system (Debian, Ubunutu,
 Zorin, etc) This script has not been widely tested across platforms
 \end{cautionbox}
 
-\begin{quote}
+\begin{clibox}[Setup Build Environment]
-{[}!cli{]} Setup Build Environment
+\begin{verbatim}
+./scripts/setup-linux-deb.sh
+\end{verbatim}
 
-\begin{Shaded}
+\end{clibox}
-\begin{Highlighting}[]
-\ExtensionTok{./scripts/setup{-}linux{-}deb.sh}
-\end{Highlighting}
-\end{Shaded}
-\end{quote}
 
 For more information on setting up the build environment for your system
 see Appendix A.

build/latex/basic-book-builder.toc

@@ -2,6 +2,6 @@
 \contentsline {chapter}{\numberline {2}Getting Started}{2}{chapter.2}%
 \contentsline {section}{\numberline {2.1}Cloning the Basic Book Builder}{2}{section.2.1}%
 \contentsline {section}{\numberline {2.2}Setting Up Build Environment}{2}{section.2.2}%
-\contentsline {chapter}{Glossary}{3}{chapter*.4}%
+\contentsline {chapter}{Glossary}{4}{chapter*.4}%
-\contentsline {chapter}{Index}{5}{chapter*.5}%
+\contentsline {chapter}{Index}{6}{chapter*.5}%
-\contentsline {chapter}{Bibliography}{7}{chapter*.6}%
+\contentsline {chapter}{Bibliography}{8}{chapter*.6}%

chapters/01_Getting_Started.md

@@ -4,7 +4,7 @@
 
 
 > [!cli] Cloning the repository
-> ```bash
+> ```
 > git clone https://github.com/jehaverlack/basic-book-builder.git
 > ```
 
@@ -14,6 +14,11 @@
 > cd basic-book-builder
 > ```
 
+> [!code] Code Example
+> ```
+> if then else
+> ```
+
 ## Setting Up Build Environment
 
 
@@ -24,7 +29,7 @@
 
 
 > [!cli] Setup Build Environment
-> ```bash
+> ```
 > ./scripts/setup-linux-deb.sh
 > ```
 

filters/callouts.lua

@@ -1,14 +1,15 @@
 -- Map callout types to LaTeX environments
 local callout_env_map = {
-    idea = "ideabox",
+  idea = "ideabox",
-    proposed = "proposedbox",
+  proposed = "proposedbox",
-    established = "establishedbox",
+  established = "establishedbox",
-    speculative = "speculativebox",
+  speculative = "speculativebox",
-    caution = "cautionbox",
+  caution = "cautionbox",
-    warning = "warningbox",
+  warning = "warningbox",
-    danger = "dangerbox"
+  danger = "dangerbox",
-  }
+  code = "codebox",
-  
+  cli = "clibox"
+}
 
 function BlockQuote(el)
   if #el.content > 0 and el.content[1].t == "Para" then

templates/header.tex

@@ -14,6 +14,8 @@
 \usepackage{xcolor}
 \definecolor{speculativeback}{RGB}{247,232,255}  % #f7e8ff
 \definecolor{speculativeframe}{RGB}{139,43,226}  % #8b2be2
+\definecolor{lightgrayback}{RGB}{245,245,245}
+\definecolor{lightgrayframe}{RGB}{180,180,180}
 
 % --- Left-align all Pandoc tables ---
 \usepackage{longtable}
@@ -113,6 +115,33 @@
   after=\par\vspace{6pt}
 }
 
+
+% =========================================================
+% Code / CLI Boxes
+% =========================================================
+
+\newtcolorbox{codebox}[1][Code]{%
+  title=\ifstrempty{#1}{\blanktitle}{#1},
+  colback=lightgrayback,
+  colframe=lightgrayframe,
+  colbacktitle=lightgrayback!90!white,
+  fonttitle=\bfseries,
+  coltitle=black,
+  enhanced, sharp corners, breakable,
+  after=\par\vspace{6pt}
+}
+
+\newtcolorbox{clibox}[1][Command Line]{%
+  title=\ifstrempty{#1}{\blanktitle}{#1},
+  colback=lightgrayback,
+  colframe=lightgrayframe,
+  colbacktitle=lightgrayback!90!white,
+  fonttitle=\bfseries,
+  coltitle=black,
+  enhanced, sharp corners, breakable,
+  after=\par\vspace{6pt}
+}
+
 \usepackage{xurl}
 
 \usepackage{fancyhdr}