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<!doctype html>
<html lang="en" class="no-js">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
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<title>CLI Reference - CodeGraphContext</title>
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background: rgba(255, 255, 255, 0.15);
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background: rgba(255, 255, 255, 0.25);
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CodeGraphContext
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CLI Reference
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<a href="https://github.com/CodeGraphContext/CodeGraphContext" title="Go to repository" class="md-source" data-md-component="source">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 7.1.0 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2025 Fonticons, Inc.--><path d="M439.6 236.1 244 40.5c-5.4-5.5-12.8-8.5-20.4-8.5s-15 3-20.4 8.4L162.5 81l51.5 51.5c27.1-9.1 52.7 16.8 43.4 43.7l49.7 49.7c34.2-11.8 61.2 31 35.5 56.7-26.5 26.5-70.2-2.9-56-37.3L240.3 199v121.9c25.3 12.5 22.3 41.8 9.1 55-6.4 6.4-15.2 10.1-24.3 10.1s-17.8-3.6-24.3-10.1c-17.6-17.6-11.1-46.9 11.2-56v-123c-20.8-8.5-24.6-30.7-18.6-45L142.6 101 8.5 235.1C3 240.6 0 247.9 0 255.5s3 15 8.5 20.4l195.6 195.7c5.4 5.4 12.7 8.4 20.4 8.4s15-3 20.4-8.4l194.7-194.7c5.4-5.4 8.4-12.8 8.4-20.4s-3-15-8.4-20.4"/></svg>
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<div class="rw-main-content md-typeset">
<h1 id="cli-command-reference">CLI Command Reference</h1>
<p>The <code>cgc</code> command-line interface is the entry point for indexing code, running graph queries, managing contexts, and administering database backends.</p>
<p>Run <code>cgc --help</code> or <code>cgc help</code> for the live command tree on your installed version.</p>
<hr />
<h2 id="global-options">Global Options</h2>
<p>These flags apply to most subcommands:</p>
<table>
<thead>
<tr>
<th style="text-align: left;">Option</th>
<th style="text-align: left;">Shorthand</th>
<th style="text-align: left;">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;"><code>--database</code></td>
<td style="text-align: left;"><code>--db</code>, <code>-db</code></td>
<td style="text-align: left;">Override the active backend for this invocation (<code>neo4j</code>, <code>falkordb</code>, <code>falkordb-remote</code>, <code>kuzudb</code>, <code>nornic</code>, <code>ladybugdb</code>).</td>
</tr>
<tr>
<td style="text-align: left;"><code>--db-path</code></td>
<td style="text-align: left;"></td>
<td style="text-align: left;">Override the on-disk storage directory for embedded engines.</td>
</tr>
<tr>
<td style="text-align: left;"><code>--context</code></td>
<td style="text-align: left;"><code>-c</code></td>
<td style="text-align: left;">Target a named context workspace.</td>
</tr>
<tr>
<td style="text-align: left;"><code>--visual</code></td>
<td style="text-align: left;"><code>--viz</code>, <code>-V</code></td>
<td style="text-align: left;">Open results in the interactive graph visualization UI.</td>
</tr>
<tr>
<td style="text-align: left;"><code>--version</code></td>
<td style="text-align: left;"><code>-v</code></td>
<td style="text-align: left;">Print package version and exit.</td>
</tr>
<tr>
<td style="text-align: left;"><code>--help</code></td>
<td style="text-align: left;"><code>-h</code></td>
<td style="text-align: left;">Show help and exit.</td>
</tr>
</tbody>
</table>
<p>Use <code>cgc version</code> (or <code>cgc --version</code>) to print the installed release (currently <strong>0.5.0</strong>).</p>
<hr />
<h2 id="core-index-lifecycle">Core Index & Lifecycle</h2>
<table>
<thead>
<tr>
<th style="text-align: left;">Command</th>
<th style="text-align: left;">Usage</th>
<th style="text-align: left;">Notes</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;"><strong><code>index</code></strong></td>
<td style="text-align: left;"><code>cgc index [PATH] [--force] [--dependency]</code></td>
<td style="text-align: left;">Shortcut: <code>cgc i</code>. Incremental by default; <code>--force</code> rebuilds from scratch.</td>
</tr>
<tr>
<td style="text-align: left;"><strong><code>clean</code></strong></td>
<td style="text-align: left;"><code>cgc clean</code></td>
<td style="text-align: left;">Purges orphaned nodes and dangling relationships.</td>
</tr>
<tr>
<td style="text-align: left;"><strong><code>stats</code></strong></td>
<td style="text-align: left;"><code>cgc stats</code></td>
<td style="text-align: left;">Repository and node counts for the active context.</td>
</tr>
<tr>
<td style="text-align: left;"><strong><code>delete</code></strong></td>
<td style="text-align: left;"><code>cgc delete <repo_path></code></td>
<td style="text-align: left;">Shortcut: <code>cgc rm</code>. Removes one indexed repository.</td>
</tr>
<tr>
<td style="text-align: left;"><strong><code>list</code></strong></td>
<td style="text-align: left;"><code>cgc list</code></td>
<td style="text-align: left;">Shortcut: <code>cgc ls</code>. Lists indexed repositories.</td>
</tr>
<tr>
<td style="text-align: left;"><strong><code>add-package</code></strong></td>
<td style="text-align: left;"><code>cgc add-package <name> <language></code></td>
<td style="text-align: left;">Indexes an installed third-party package as a dependency graph.</td>
</tr>
</tbody>
</table>
<hr />
<h2 id="search-find">Search (<code>find</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>find<span class="w"> </span><subcommand><span class="w"> </span><span class="o">[</span>args<span class="o">]</span><span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
</code></pre></div>
<table>
<thead>
<tr>
<th style="text-align: left;">Subcommand</th>
<th style="text-align: left;">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;"><code>find name <symbol></code></td>
<td style="text-align: left;">Search by symbol name. Options: <code>--type function\|class\|file\|module</code>, <code>--fuzzy</code> / <code>--no-fuzzy</code>.</td>
</tr>
<tr>
<td style="text-align: left;"><code>find pattern <regex></code></td>
<td style="text-align: left;">Regex search across indexed source.</td>
</tr>
<tr>
<td style="text-align: left;"><code>find type <node_type></code></td>
<td style="text-align: left;">List nodes of a given label (e.g. <code>Function</code>, <code>Class</code>).</td>
</tr>
<tr>
<td style="text-align: left;"><code>find content <text></code></td>
<td style="text-align: left;">Full-text / substring search in source and docstrings. Neo4j uses Lucene; embedded backends use portable substring matching.</td>
</tr>
<tr>
<td style="text-align: left;"><code>find decorator <name></code></td>
<td style="text-align: left;">Functions with a given decorator.</td>
</tr>
<tr>
<td style="text-align: left;"><code>find argument <name></code></td>
<td style="text-align: left;">Functions declaring a parameter name.</td>
</tr>
<tr>
<td style="text-align: left;"><code>find variable <name></code></td>
<td style="text-align: left;">Variable references and assignments.</td>
</tr>
</tbody>
</table>
<hr />
<h2 id="analysis-analyze">Analysis (<code>analyze</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>analyze<span class="w"> </span><subcommand><span class="w"> </span><span class="o">[</span>args<span class="o">]</span><span class="w"> </span><span class="o">[</span>options<span class="o">]</span>
</code></pre></div>
<table>
<thead>
<tr>
<th style="text-align: left;">Subcommand</th>
<th style="text-align: left;">Description</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;"><code>analyze callers <function></code></td>
<td style="text-align: left;">Direct callers of a function.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze calls <function></code></td>
<td style="text-align: left;">Direct callees of a function.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze chain <source> <target></code></td>
<td style="text-align: left;">Shortest call path between two symbols.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze deps <module></code></td>
<td style="text-align: left;">Module import dependencies.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze tree <class></code></td>
<td style="text-align: left;">Class inheritance tree.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze complexity <function></code></td>
<td style="text-align: left;">Cyclomatic complexity for one function.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze dead-code</code></td>
<td style="text-align: left;">Unreferenced functions/files (with optional filters).</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze overrides <class></code></td>
<td style="text-align: left;">Methods overridden in subclasses.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze variable <name></code></td>
<td style="text-align: left;">Variable scope and modification sites.</td>
</tr>
<tr>
<td style="text-align: left;"><code>analyze kotlin-call-audit</code></td>
<td style="text-align: left;">Kotlin-specific call resolution audit.</td>
</tr>
</tbody>
</table>
<hr />
<h2 id="querying-reports">Querying & Reports</h2>
<h4 id="query"><code>query</code></h4>
<p>Execute a read-only Cypher query.</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>query<span class="w"> </span><span class="s2">"MATCH (f:Function) RETURN f.name LIMIT 10"</span>
cgc<span class="w"> </span>query<span class="w"> </span><span class="s2">"MATCH (n)-[r]->(m) RETURN n,r,m LIMIT 50"</span><span class="w"> </span>--visual
</code></pre></div>
<p><code>cgc cypher</code> still works as a hidden alias but prints a deprecation warning—prefer <code>cgc query</code>.</p>
<h4 id="report"><code>report</code></h4>
<p>Generate <code>CGC_REPORT.md</code> with god-node, complexity, and coupling metrics.</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>report<span class="w"> </span><span class="o">[</span>--include-java<span class="o">]</span>
</code></pre></div>
<h4 id="visualize"><code>visualize</code></h4>
<p>Launch the React force-directed graph UI (shortcut: <code>cgc v</code>).</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>visualize<span class="w"> </span><span class="o">[</span>--repo<span class="w"> </span><path><span class="o">]</span><span class="w"> </span><span class="o">[</span>--port<span class="w"> </span><span class="m">8000</span><span class="o">]</span>
</code></pre></div>
<hr />
<h2 id="context-workspaces-context">Context Workspaces (<code>context</code>)</h2>
<p>Manage isolation modes and named workspaces. See <a href="../../guides/contexts/">Configuration Contexts</a>.</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>context<span class="w"> </span>list
cgc<span class="w"> </span>context<span class="w"> </span>mode<span class="w"> </span><global<span class="p">|</span>per-repo<span class="p">|</span>named>
cgc<span class="w"> </span>context<span class="w"> </span>create<span class="w"> </span><name><span class="w"> </span><span class="o">[</span>--database<span class="w"> </span>kuzudb<span class="o">]</span><span class="w"> </span><span class="o">[</span>--db-path<span class="w"> </span>/path<span class="o">]</span>
cgc<span class="w"> </span>context<span class="w"> </span>delete<span class="w"> </span><name>
cgc<span class="w"> </span>context<span class="w"> </span>default<span class="w"> </span><name>
</code></pre></div>
<hr />
<h2 id="configuration-config">Configuration (<code>config</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>config<span class="w"> </span>show
cgc<span class="w"> </span>config<span class="w"> </span><span class="nb">set</span><span class="w"> </span><KEY><span class="w"> </span><VALUE>
cgc<span class="w"> </span>config<span class="w"> </span>db<span class="w"> </span><backend>
cgc<span class="w"> </span>config<span class="w"> </span>reset
</code></pre></div>
<p>Valid backends: <code>kuzudb</code>, <code>ladybugdb</code>, <code>falkordb</code>, <code>falkordb-remote</code>, <code>neo4j</code>, <code>nornic</code>. See <a href="../config/">Configuration Reference</a>.</p>
<hr />
<h2 id="mcp-neo4j-setup">MCP & Neo4j Setup</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>mcp<span class="w"> </span>setup<span class="w"> </span><span class="c1"># Interactive IDE wizard (shortcut: cgc m)</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>start<span class="w"> </span><span class="c1"># Start stdio MCP server</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>tools<span class="w"> </span><span class="c1"># List registered MCP tools</span>
cgc<span class="w"> </span>neo4j<span class="w"> </span>setup<span class="w"> </span><span class="c1"># Neo4j connection wizard (shortcut: cgc n)</span>
</code></pre></div>
<hr />
<h2 id="portable-bundles-bundle">Portable Bundles (<code>bundle</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>bundle<span class="w"> </span><span class="nb">export</span><span class="w"> </span><output.cgc><span class="w"> </span><span class="o">[</span>--repo<span class="w"> </span>PATH<span class="o">]</span><span class="w"> </span><span class="o">[</span>--no-stats<span class="o">]</span><span class="w"> </span><span class="o">[</span>--context<span class="w"> </span>NAME<span class="o">]</span>
cgc<span class="w"> </span>bundle<span class="w"> </span>import<span class="w"> </span><file.cgc><span class="w"> </span><span class="o">[</span>--clear<span class="o">]</span><span class="w"> </span><span class="o">[</span>--yes<span class="p">|</span>-y<span class="o">]</span><span class="w"> </span><span class="o">[</span>--context<span class="w"> </span>NAME<span class="o">]</span>
cgc<span class="w"> </span>bundle<span class="w"> </span>load<span class="w"> </span><name><span class="w"> </span><span class="o">[</span>--clear<span class="o">]</span><span class="w"> </span><span class="o">[</span>--yes<span class="p">|</span>-y<span class="o">]</span>
<span class="c1"># Shortcuts</span>
cgc<span class="w"> </span><span class="nb">export</span><span class="w"> </span>my-project.cgc<span class="w"> </span>--repo<span class="w"> </span>/path/to/project
cgc<span class="w"> </span>load<span class="w"> </span>numpy
</code></pre></div>
<p>Use <code>--yes</code> / <code>-y</code> with <code>--clear</code> to skip the destructive-import confirmation (required in CI/non-interactive shells).</p>
<h4 id="registry"><code>registry</code></h4>
<p>Browse and download pre-indexed bundles.</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>registry<span class="w"> </span>list<span class="w"> </span><span class="o">[</span>--verbose<span class="o">]</span><span class="w"> </span><span class="o">[</span>--unique<span class="o">]</span>
cgc<span class="w"> </span>registry<span class="w"> </span>search<span class="w"> </span><query>
cgc<span class="w"> </span>registry<span class="w"> </span>download<span class="w"> </span><name><span class="w"> </span><span class="o">[</span>--output<span class="w"> </span>DIR<span class="o">]</span><span class="w"> </span><span class="o">[</span>--load<span class="o">]</span>
cgc<span class="w"> </span>registry<span class="w"> </span>request<span class="w"> </span><github_url>
</code></pre></div>
<hr />
<h2 id="real-time-watchers">Real-Time Watchers</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>watch<span class="w"> </span><span class="o">[</span>PATH<span class="o">]</span><span class="w"> </span><span class="c1"># Shortcut: cgc w</span>
cgc<span class="w"> </span>unwatch<span class="w"> </span><PATH>
cgc<span class="w"> </span>watching
</code></pre></div>
<p>On startup, watchers reconcile the graph with the filesystem (add missing files, remove deleted paths) before monitoring changes.</p>
<hr />
<h2 id="git-hooks-hook">Git Hooks (<code>hook</code>)</h2>
<p>Keep the graph in sync on commit:</p>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>hook<span class="w"> </span>install<span class="w"> </span><span class="o">[</span>PATH<span class="o">]</span><span class="w"> </span><span class="o">[</span>--force<span class="o">]</span>
cgc<span class="w"> </span>hook<span class="w"> </span>uninstall<span class="w"> </span><span class="o">[</span>PATH<span class="o">]</span>
cgc<span class="w"> </span>hook<span class="w"> </span>status<span class="w"> </span><span class="o">[</span>PATH<span class="o">]</span>
</code></pre></div>
<hr />
<h2 id="http-api-gateway-api">HTTP API Gateway (<code>api</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>api<span class="w"> </span>start<span class="w"> </span><span class="o">[</span>--host<span class="w"> </span><span class="m">0</span>.0.0.0<span class="o">]</span><span class="w"> </span><span class="o">[</span>--port<span class="w"> </span><span class="m">8000</span><span class="o">]</span><span class="w"> </span><span class="o">[</span>--reload<span class="o">]</span>
</code></pre></div>
<p>Exposes REST endpoints under <code>/api/v1</code> and a liveness probe at <code>GET /health</code>. See <a href="../api/">HTTP API Reference</a>.</p>
<hr />
<h2 id="external-datasources-datasource">External Datasources (<code>datasource</code>)</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>datasource<span class="w"> </span>mysql
cgc<span class="w"> </span>datasource<span class="w"> </span>cassandra
cgc<span class="w"> </span>datasource<span class="w"> </span>redis
</code></pre></div>
<hr />
<h2 id="scip-setup">SCIP Setup</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>setup-scip
</code></pre></div>
<p>Installs or verifies external SCIP indexers when <code>SCIP_INDEXER=true</code>. C/C++ require <code>compile_commands.json</code>; see the README SCIP section.</p>
<hr />
<h2 id="system-diagnostics">System Diagnostics</h2>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>doctor
</code></pre></div>
<p>Checks configuration, database connectivity, Tree-sitter parsers, dependencies, and file permissions.</p>
<hr />
<h2 id="command-shortcuts">Command Shortcuts</h2>
<table>
<thead>
<tr>
<th style="text-align: left;">Shortcut</th>
<th style="text-align: left;">Full command</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align: left;"><code>cgc i</code></td>
<td style="text-align: left;"><code>cgc index</code></td>
</tr>
<tr>
<td style="text-align: left;"><code>cgc ls</code></td>