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Step 1: Install CodeGraphContext
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Step 2: Choose Database Backend (Optional)
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Step 3: Index Your First Repository
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Step 4: Verify Setup
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Step 1-3: Same as CLI Users
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Step 4: Configure MCP Integration
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Step 5: Start MCP Server
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Step 6: Verify MCP Integration
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Typical Daily Workflow
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During Development: Natural Language Queries
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Issue 1: cgc command not found
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<h1 id="setup-workflows-codegraphcontext">Setup Workflows - CodeGraphContext</h1>
<p>This document provides <strong>exact, step-by-step workflows</strong> for setting up and using CodeGraphContext, both for first-time setup and everyday use.</p>
<hr />
<h2 id="table-of-contents">Table of Contents</h2>
<ol>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#first-time-setup-cli-users">First-Time Setup: CLI Users</a></li>
<li><a href="#first-time-setup-mcp-users">First-Time Setup: MCP Users</a></li>
<li><a href="#every-time-workflow-cli-users">Every-Time Workflow: CLI Users</a></li>
<li><a href="#every-time-workflow-mcp-users">Every-Time Workflow: MCP Users</a></li>
<li><a href="#troubleshooting">Troubleshooting</a></li>
</ol>
<hr />
<h2 id="prerequisites">Prerequisites</h2>
<h3 id="required">Required</h3>
<ul>
<li><strong>Python 3.8+</strong> installed on your system</li>
<li><strong>pip</strong> package manager</li>
<li><strong>Git</strong> (for cloning repositories)</li>
</ul>
<h3 id="optional-for-advanced-features">Optional (for advanced features)</h3>
<ul>
<li><strong>Neo4j</strong> (for large-scale repositories > 100k LOC)</li>
<li><strong>Docker</strong> (for containerized deployment)</li>
</ul>
<h3 id="check-prerequisites">Check Prerequisites</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Check Python version</span>
python<span class="w"> </span>--version
<span class="c1"># Expected: Python 3.8.0 or higher</span>
<span class="c1"># Check pip</span>
pip<span class="w"> </span>--version
<span class="c1"># Expected: pip 20.0.0 or higher</span>
<span class="c1"># Check git</span>
git<span class="w"> </span>--version
<span class="c1"># Expected: git version 2.0.0 or higher</span>
</code></pre></div>
<hr />
<h2 id="first-time-setup-cli-users">First-Time Setup: CLI Users</h2>
<p><strong>Time Required</strong>: 5-10 minutes<br />
<strong>Frequency</strong>: Once per machine</p>
<h3 id="step-1-install-codegraphcontext">Step 1: Install CodeGraphContext</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Install via pip</span>
pip<span class="w"> </span>install<span class="w"> </span>codegraphcontext
<span class="c1"># Verify installation</span>
cgc<span class="w"> </span>--version
<span class="c1"># Expected output:</span>
<span class="c1"># CodeGraphContext version 1.0.0</span>
</code></pre></div>
<p><strong>Troubleshooting</strong>: If <code>cgc</code> command not found, add Python scripts to PATH:
<div class="highlight"><pre><span></span><code><span class="c1"># Linux/Mac</span>
<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.local/bin:</span><span class="nv">$PATH</span><span class="s2">"</span>
<span class="c1"># Windows</span>
<span class="c1"># Add %APPDATA%\Python\Scripts to PATH</span>
</code></pre></div></p>
<h3 id="step-2-choose-database-backend-optional">Step 2: Choose Database Backend (Optional)</h3>
<p>CodeGraphContext automatically uses <strong>FalkorDB</strong> (embedded, no setup needed) for most use cases.</p>
<p><strong>When to use Neo4j instead:</strong>
- Repository > 100,000 lines of code
- Need to share graph across team members
- Want persistent storage across machines</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Option A: Use FalkorDB (default, recommended for most users)</span>
<span class="c1"># No action needed - works out of the box</span>
<span class="c1"># Option B: Setup Neo4j (for large repositories)</span>
cgc<span class="w"> </span>neo4j<span class="w"> </span>setup
<span class="c1"># This will:</span>
<span class="c1"># 1. Check if Neo4j is installed</span>
<span class="c1"># 2. If not, provide installation instructions</span>
<span class="c1"># 3. Configure connection settings</span>
<span class="c1"># 4. Test the connection</span>
</code></pre></div>
<p><strong>Neo4j Setup Output:</strong>
<div class="highlight"><pre><span></span><code>Checking for Neo4j installation...
✗ Neo4j not found
Would you like to install Neo4j? (y/n): y
Installing Neo4j...
✓ Neo4j 5.x installed
✓ Started Neo4j service
✓ Default credentials: neo4j/neo4j
Please change the default password:
New password: ********
Confirm password: ********
✓ Password updated
✓ Connection tested successfully
Configuration saved to: ~/.cgc/config.yml
</code></pre></div></p>
<h3 id="step-3-index-your-first-repository">Step 3: Index Your First Repository</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Navigate to your project</span>
<span class="nb">cd</span><span class="w"> </span>~/projects/my-project
<span class="c1"># Index the repository</span>
cgc<span class="w"> </span>index<span class="w"> </span>.
<span class="c1"># Expected output:</span>
<span class="c1"># Indexing repository: /home/user/projects/my-project</span>
<span class="c1"># ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━</span>
<span class="c1"># Scanning files... ✓ 1,247 files found</span>
<span class="c1"># Parsing Python files... ✓ 892 files (71%)</span>
<span class="c1"># Parsing JavaScript... ✓ 234 files (19%)</span>
<span class="c1"># Parsing TypeScript... ✓ 121 files (10%)</span>
<span class="c1"># </span>
<span class="c1"># Building graph...</span>
<span class="c1"># ✓ Created 3,421 function nodes</span>
<span class="c1"># ✓ Created 892 class nodes</span>
<span class="c1"># ✓ Created 234 module nodes</span>
<span class="c1"># ✓ Created 15,234 relationships</span>
<span class="c1"># </span>
<span class="c1"># Database: FalkorDB (embedded)</span>
<span class="c1"># Indexing completed in 23.4 seconds</span>
</code></pre></div>
<h3 id="step-4-verify-setup">Step 4: Verify Setup</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Check repository statistics</span>
cgc<span class="w"> </span>stats
<span class="c1"># Expected output:</span>
<span class="c1"># Repository Statistics</span>
<span class="c1"># ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━</span>
<span class="c1"># Repository: my-project</span>
<span class="c1"># Path: /home/user/projects/my-project</span>
<span class="c1"># </span>
<span class="c1"># Code Elements:</span>
<span class="c1"># Files: 1,247</span>
<span class="c1"># Functions: 3,421</span>
<span class="c1"># Classes: 892</span>
<span class="c1"># Modules: 234</span>
<span class="c1"># </span>
<span class="c1"># Relationships:</span>
<span class="c1"># Function calls: 8,234</span>
<span class="c1"># Imports: 2,456</span>
<span class="c1"># Inheritance: 234</span>
<span class="c1"># Total: 15,234</span>
<span class="c1"># </span>
<span class="c1"># Database: FalkorDB</span>
<span class="c1"># Last indexed: 2026-01-30 01:15:23</span>
</code></pre></div>
<div class="highlight"><pre><span></span><code><span class="c1"># Try a simple query</span>
cgc<span class="w"> </span>find<span class="w"> </span><span class="s2">"main"</span><span class="w"> </span>--type<span class="w"> </span><span class="k">function</span>
<span class="c1"># Expected output:</span>
<span class="c1"># Found 5 functions matching 'main':</span>
<span class="c1"># </span>
<span class="c1"># 1. main</span>
<span class="c1"># File: src/app.py:123</span>
<span class="c1"># </span>
<span class="c1"># 2. main_loop</span>
<span class="c1"># File: src/core/event_loop.py:45</span>
<span class="c1"># </span>
<span class="c1"># ... (3 more)</span>
</code></pre></div>
<h3 id="step-5-explore-available-commands">Step 5: Explore Available Commands</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># See all available commands</span>
cgc<span class="w"> </span><span class="nb">help</span>
<span class="c1"># Expected output:</span>
<span class="c1"># CodeGraphContext CLI</span>
<span class="c1"># </span>
<span class="c1"># Usage: cgc [COMMAND] [OPTIONS]</span>
<span class="c1"># </span>
<span class="c1"># Project Management:</span>
<span class="c1"># index [PATH] Index a repository</span>
<span class="c1"># reindex Re-index current repository</span>
<span class="c1"># stats Show repository statistics</span>
<span class="c1"># clean Clear the database</span>
<span class="c1"># </span>
<span class="c1"># Code Discovery:</span>
<span class="c1"># find <query> Search for code elements</span>
<span class="c1"># visualize Generate architecture visualization</span>
<span class="c1"># </span>
<span class="c1"># Code Analysis:</span>
<span class="c1"># analyze callers <name> Find who calls a function</span>
<span class="c1"># analyze callees <name> Find what a function calls</span>
<span class="c1"># analyze chain <a> <b> Show call chain between functions</span>
<span class="c1"># analyze deps <module> Show module dependencies</span>
<span class="c1"># analyze dead-code Find unused functions</span>
<span class="c1"># analyze complexity Find complex functions</span>
<span class="c1"># </span>
<span class="c1"># ... (more commands)</span>
</code></pre></div>
<p><strong>✅ Setup Complete!</strong> You're ready to use CodeGraphContext.</p>
<hr />
<h2 id="first-time-setup-mcp-users">First-Time Setup: MCP Users</h2>
<p><strong>Time Required</strong>: 10-15 minutes<br />
<strong>Frequency</strong>: Once per machine</p>
<h3 id="step-1-3-same-as-cli-users">Step 1-3: Same as CLI Users</h3>
<p>Follow Steps 1-3 from <a href="#first-time-setup-cli-users">First-Time Setup: CLI Users</a></p>
<h3 id="step-4-configure-mcp-integration">Step 4: Configure MCP Integration</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Setup MCP configuration</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>setup
<span class="c1"># Interactive prompts:</span>
<span class="c1"># </span>
<span class="c1"># Select your IDE/Editor:</span>
<span class="c1"># 1. Cursor</span>
<span class="c1"># 2. VS Code (with Continue.dev)</span>
<span class="c1"># 3. Claude Desktop</span>
<span class="c1"># 4. Custom (manual configuration)</span>
<span class="c1"># </span>
<span class="c1"># Choice: 1</span>
</code></pre></div>
<p><strong>For Cursor:</strong>
<div class="highlight"><pre><span></span><code>Configuring MCP for Cursor...
✓ Found Cursor config at: ~/.config/cursor/mcp.json
✓ Added CodeGraphContext MCP server
✓ Server command: cgc mcp start
Configuration:
{
"mcpServers": {
"codegraphcontext": {
"command": "cgc",
"args": ["mcp", "start"],
"env": {
"CGC_DB": "falkordb"
}
}
}
}
✓ Configuration saved
Next steps:
1. Restart Cursor
2. Open Command Palette (Cmd/Ctrl + Shift + P)
3. Run: "MCP: Reload Servers"
4. Verify CodeGraphContext appears in MCP server list
</code></pre></div></p>
<p><strong>For VS Code (Continue.dev):</strong>
<div class="highlight"><pre><span></span><code>Configuring MCP for VS Code (Continue.dev)...
✓ Found Continue config at: ~/.continue/config.json
✓ Added CodeGraphContext MCP server
Next steps:
1. Restart VS Code
2. Open Continue sidebar
3. Verify CodeGraphContext tools are available
</code></pre></div></p>
<p><strong>For Claude Desktop:</strong>
<div class="highlight"><pre><span></span><code>Configuring MCP for Claude Desktop...
✓ Created config at: ~/Library/Application Support/Claude/claude_desktop_config.json
Next steps:
1. Restart Claude Desktop
2. Start a new conversation
3. Ask: "What MCP tools do you have access to?"
4. Verify CodeGraphContext tools are listed
</code></pre></div></p>
<h3 id="step-5-start-mcp-server">Step 5: Start MCP Server</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Start the MCP server</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Expected output:</span>
<span class="c1"># CodeGraphContext MCP Server</span>
<span class="c1"># ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━</span>
<span class="c1"># ✓ Server started</span>
<span class="c1"># ✓ Protocol: Model Context Protocol (MCP)</span>
<span class="c1"># ✓ Transport: stdio</span>
<span class="c1"># ✓ Database: FalkorDB connected</span>
<span class="c1"># ✓ Repository: /home/user/projects/my-project</span>
<span class="c1"># ✓ Watching for file changes: enabled</span>
<span class="c1"># </span>
<span class="c1"># Available tools: 18</span>
<span class="c1"># - find_code</span>
<span class="c1"># - analyze_code_relationships</span>
<span class="c1"># - find_dead_code</span>
<span class="c1"># - execute_cypher_query</span>
<span class="c1"># ... (14 more)</span>
<span class="c1"># </span>
<span class="c1"># Server ready. Listening for requests...</span>
</code></pre></div>
<p><strong>Note</strong>: Keep this terminal open, or run in background:</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Run in background (Linux/Mac)</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>start<span class="w"> </span><span class="p">&</span>
<span class="c1"># Or use tmux/screen for persistent session</span>
tmux<span class="w"> </span>new<span class="w"> </span>-s<span class="w"> </span>cgc
cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Press Ctrl+B, then D to detach</span>
</code></pre></div>
<h3 id="step-6-verify-mcp-integration">Step 6: Verify MCP Integration</h3>
<p><strong>In Cursor/VS Code:</strong></p>
<ol>
<li>Open your IDE</li>
<li>Start a new chat with AI assistant</li>
<li>Ask: "What CodeGraphContext tools do you have?"</li>
</ol>
<p><strong>Expected AI Response:</strong></p>
<blockquote>
<p>"I have access to 18 CodeGraphContext tools:</p>
<p><strong>Code Discovery:</strong>
- find_code - Search for functions, classes, files
- list_indexed_repositories - Show indexed projects</p>
<p><strong>Code Analysis:</strong>
- analyze_code_relationships - Find callers, callees, call chains
- find_dead_code - Find unused functions
- find_most_complex_functions - Find complex code
- calculate_cyclomatic_complexity - Measure function complexity</p>
<p><strong>Graph Queries:</strong>
- execute_cypher_query - Run custom graph queries
- visualize_graph_query - Generate graph visualizations</p>
<p>... (10 more tools)</p>
<p>How can I help you explore your codebase?"</p>
</blockquote>
<p><strong>Test with a real query:</strong></p>
<p>Ask AI: "Find all functions that call <code>authenticate</code>"</p>
<p><strong>Expected AI Response:</strong></p>
<blockquote>
<p>"I found 12 functions that call <code>authenticate</code>:</p>
<p><strong>Direct callers (3):</strong>
1. <code>login</code> in api/auth.py:45
2. <code>verify_token</code> in middleware/auth.py:89
3. <code>refresh_session</code> in api/session.py:123</p>
<p><strong>Indirect callers (9 more):</strong>
... (AI lists them)</p>
<p>Would you like me to show the call chain for any of these?"</p>
</blockquote>
<p><strong>✅ MCP Setup Complete!</strong> Your AI assistant now has code intelligence.</p>
<hr />
<h2 id="every-time-workflow-cli-users">Every-Time Workflow: CLI Users</h2>
<p><strong>Time Required</strong>: 2-5 minutes per session<br />
<strong>Frequency</strong>: Daily/as needed</p>
<h3 id="typical-daily-workflow">Typical Daily Workflow</h3>
<h4 id="morning-start-of-day"><strong>Morning: Start of Day</strong></h4>
<div class="highlight"><pre><span></span><code><span class="c1"># 1. Navigate to your project</span>
<span class="nb">cd</span><span class="w"> </span>~/projects/my-project
<span class="c1"># 2. Pull latest changes</span>
git<span class="w"> </span>pull<span class="w"> </span>origin<span class="w"> </span>main
<span class="c1"># 3. Update the code graph (if files changed)</span>
cgc<span class="w"> </span>reindex
<span class="c1"># Output:</span>
<span class="c1"># Detecting changes...</span>
<span class="c1"># ✓ 12 files modified</span>
<span class="c1"># ✓ 3 files added</span>
<span class="c1"># ✓ 1 file deleted</span>
<span class="c1"># </span>
<span class="c1"># Updating graph...</span>
<span class="c1"># ✓ Updated 45 nodes</span>
<span class="c1"># ✓ Updated 123 relationships</span>
<span class="c1"># </span>
<span class="c1"># Reindexing completed in 3.2 seconds</span>
</code></pre></div>
<p><strong>Alternative</strong>: Use auto-watch mode (set once, forget it)</p>
<div class="highlight"><pre><span></span><code><span class="c1"># Enable auto-watch for this repository</span>
cgc<span class="w"> </span>watch<span class="w"> </span>.
<span class="c1"># Output:</span>
<span class="c1"># ✓ Watching: /home/user/projects/my-project</span>
<span class="c1"># ✓ Auto-reindex on file changes: enabled</span>
<span class="c1"># </span>
<span class="c1"># The graph will automatically update when files change.</span>
<span class="c1"># Press Ctrl+C to stop watching.</span>
</code></pre></div>
<h4 id="during-development-common-tasks"><strong>During Development: Common Tasks</strong></h4>
<p><strong>Task 1: Understanding a new feature</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Find the entry point</span>
cgc<span class="w"> </span>find<span class="w"> </span><span class="s2">"handle_payment"</span><span class="w"> </span>--type<span class="w"> </span><span class="k">function</span>
<span class="c1"># See what it calls</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callees<span class="w"> </span>handle_payment
<span class="c1"># See the full execution flow</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>chain<span class="w"> </span>handle_payment<span class="w"> </span>process_payment
</code></pre></div>
<p><strong>Task 2: Before refactoring</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Find all usages of a function</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callers<span class="w"> </span>calculate_total
<span class="c1"># Check complexity</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>complexity<span class="w"> </span>calculate_total
<span class="c1"># Find dead code to remove first</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>dead-code
</code></pre></div>
<p><strong>Task 3: Code review</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Check what a PR changes</span>
git<span class="w"> </span>diff<span class="w"> </span>main...feature-branch<span class="w"> </span>--name-only<span class="w"> </span>><span class="w"> </span>changed_files.txt
<span class="c1"># For each changed file, check impact</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callers<span class="w"> </span>MyChangedClass
<span class="c1"># Verify test coverage</span>
cgc<span class="w"> </span>find<span class="w"> </span><span class="s2">"test_my_changed_class"</span><span class="w"> </span>--type<span class="w"> </span><span class="k">function</span>
</code></pre></div>
<p><strong>Task 4: Debugging</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Find where a variable is modified</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>modifies<span class="w"> </span>user_session
<span class="c1"># Trace execution path</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>chain<span class="w"> </span>api_endpoint<span class="w"> </span>database_query
<span class="c1"># Find similar code patterns</span>
cgc<span class="w"> </span>find<span class="w"> </span><span class="s2">"try.*except.*pass"</span><span class="w"> </span>--regex
</code></pre></div>
<h4 id="end-of-day-cleanup"><strong>End of Day: Cleanup</strong></h4>
<div class="highlight"><pre><span></span><code><span class="c1"># Optional: Clear cache if needed</span>
cgc<span class="w"> </span>clean<span class="w"> </span>--cache-only
<span class="c1"># Optional: Export graph for documentation</span>
cgc<span class="w"> </span>visualize<span class="w"> </span>--output<span class="w"> </span>daily_architecture.html
</code></pre></div>
<h3 id="quick-reference-most-used-commands">Quick Reference: Most Used Commands</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Search</span>
cgc<span class="w"> </span>find<span class="w"> </span><query><span class="w"> </span><span class="c1"># Find code elements</span>
cgc<span class="w"> </span>find<span class="w"> </span><query><span class="w"> </span>--type<span class="w"> </span><span class="k">function</span><span class="w"> </span><span class="c1"># Find only functions</span>
cgc<span class="w"> </span>find<span class="w"> </span><query><span class="w"> </span>--type<span class="w"> </span>class<span class="w"> </span><span class="c1"># Find only classes</span>
<span class="c1"># Analysis</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callers<span class="w"> </span><name><span class="w"> </span><span class="c1"># Who calls this?</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callees<span class="w"> </span><name><span class="w"> </span><span class="c1"># What does this call?</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>chain<span class="w"> </span><a><span class="w"> </span><b><span class="w"> </span><span class="c1"># Call path from A to B</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>dead-code<span class="w"> </span><span class="c1"># Find unused code</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>complexity<span class="w"> </span><span class="c1"># Find complex functions</span>
<span class="c1"># Visualization</span>
cgc<span class="w"> </span>visualize<span class="w"> </span><span class="c1"># Generate architecture diagram</span>
cgc<span class="w"> </span>stats<span class="w"> </span><span class="c1"># Show repository statistics</span>
<span class="c1"># Maintenance</span>
cgc<span class="w"> </span>reindex<span class="w"> </span><span class="c1"># Update after code changes</span>
cgc<span class="w"> </span>watch<span class="w"> </span>.<span class="w"> </span><span class="c1"># Auto-update on file changes</span>
</code></pre></div>
<hr />
<h2 id="every-time-workflow-mcp-users">Every-Time Workflow: MCP Users</h2>
<p><strong>Time Required</strong>: 1-2 minutes per session<br />
<strong>Frequency</strong>: Daily/as needed</p>
<h3 id="typical-daily-workflow_1">Typical Daily Workflow</h3>
<h4 id="morning-start-of-day_1"><strong>Morning: Start of Day</strong></h4>
<div class="highlight"><pre><span></span><code><span class="c1"># Option 1: Start MCP server manually</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Option 2: Auto-start with system (set once)</span>
<span class="c1"># Add to ~/.bashrc or ~/.zshrc:</span>
<span class="c1"># cgc mcp start &</span>
<span class="c1"># Option 3: Use tmux/screen for persistent session</span>
tmux<span class="w"> </span>attach<span class="w"> </span>-t<span class="w"> </span>cgc<span class="w"> </span><span class="o">||</span><span class="w"> </span>tmux<span class="w"> </span>new<span class="w"> </span>-s<span class="w"> </span>cgc<span class="w"> </span><span class="s2">"cgc mcp start"</span>
</code></pre></div>
<p><strong>Verify server is running:</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Check if MCP server is running</span>
ps<span class="w"> </span>aux<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span><span class="s2">"cgc mcp"</span>
<span class="c1"># Expected output:</span>
<span class="c1"># user 12345 0.1 0.5 cgc mcp start</span>
</code></pre></div>
<h4 id="during-development-natural-language-queries"><strong>During Development: Natural Language Queries</strong></h4>
<p>Open your IDE and ask your AI assistant:</p>
<p><strong>Understanding Code:</strong>
- "What does the <code>process_payment</code> function do?"
- "Show me all functions that call <code>authenticate</code>"
- "What's the call chain from the API endpoint to the database?"</p>
<p><strong>Before Refactoring:</strong>
- "What will break if I change <code>calculate_total</code>?"
- "Find all dead code in the auth module"
- "Show me the most complex functions"</p>
<p><strong>Code Review:</strong>
- "What's the impact of changing <code>UserService</code>?"
- "Are there any circular dependencies?"
- "Find all functions that access the database"</p>
<p><strong>Debugging:</strong>
- "Trace the execution from <code>handle_request</code> to <code>send_email</code>"
- "Who modifies the <code>session_state</code> variable?"
- "Find all error handling code"</p>
<h4 id="end-of-day-cleanup_1"><strong>End of Day: Cleanup</strong></h4>
<div class="highlight"><pre><span></span><code><span class="c1"># Optional: Stop MCP server if running manually</span>
<span class="c1"># Press Ctrl+C in the terminal running cgc mcp start</span>
<span class="c1"># Or kill the process</span>
pkill<span class="w"> </span>-f<span class="w"> </span><span class="s2">"cgc mcp start"</span>
</code></pre></div>
<h3 id="integration-with-ai-workflows">Integration with AI Workflows</h3>
<p><strong>Example 1: Feature Development</strong></p>
<ol>
<li><strong>Ask AI</strong>: "I need to add a new payment method. Show me how existing payment methods are implemented."</li>
<li><strong>AI uses CGC</strong>: Finds <code>PaymentMethod</code> class, shows all implementations</li>
<li><strong>AI generates</strong>: Boilerplate code following existing patterns</li>
<li><strong>You review</strong>: AI-generated code with full context</li>
</ol>
<p><strong>Example 2: Bug Investigation</strong></p>
<ol>
<li><strong>Ask AI</strong>: "Users report checkout fails for international orders. Help me debug."</li>
<li><strong>AI uses CGC</strong>: Traces call chain from checkout to payment processing</li>
<li><strong>AI identifies</strong>: Missing email notification call (like in User Journey #2)</li>
<li><strong>AI suggests</strong>: Exact fix with line numbers</li>
</ol>
<p><strong>Example 3: Refactoring</strong></p>
<ol>
<li><strong>Ask AI</strong>: "I want to refactor <code>OldAuthService</code> to <code>NewAuthService</code>. Create a migration plan."</li>
<li><strong>AI uses CGC</strong>: Finds all 47 usages, analyzes complexity</li>
<li><strong>AI generates</strong>: Step-by-step migration plan with risk assessment</li>
<li><strong>You execute</strong>: Safe, incremental migration</li>
</ol>
<hr />
<h2 id="troubleshooting">Troubleshooting</h2>
<h3 id="common-issues">Common Issues</h3>
<h4 id="issue-1-cgc-command-not-found"><strong>Issue 1: <code>cgc</code> command not found</strong></h4>
<p><strong>Symptoms:</strong>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>--version
<span class="c1"># bash: cgc: command not found</span>
</code></pre></div></p>
<p><strong>Solution:</strong>
<div class="highlight"><pre><span></span><code><span class="c1"># Find where pip installed cgc</span>
pip<span class="w"> </span>show<span class="w"> </span>codegraphcontext<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span>Location
<span class="c1"># Add to PATH</span>
<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span><span class="s2">"</span><span class="nv">$HOME</span><span class="s2">/.local/bin:</span><span class="nv">$PATH</span><span class="s2">"</span>
<span class="c1"># Make permanent (add to ~/.bashrc or ~/.zshrc)</span>
<span class="nb">echo</span><span class="w"> </span><span class="s1">'export PATH="$HOME/.local/bin:$PATH"'</span><span class="w"> </span>>><span class="w"> </span>~/.bashrc
<span class="nb">source</span><span class="w"> </span>~/.bashrc
</code></pre></div></p>
<h4 id="issue-2-indexing-fails-with-permission-denied"><strong>Issue 2: Indexing fails with "Permission denied"</strong></h4>
<p><strong>Symptoms:</strong>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>index<span class="w"> </span>.
<span class="c1"># Error: Permission denied: /some/file.py</span>
</code></pre></div></p>
<p><strong>Solution:</strong>
<div class="highlight"><pre><span></span><code><span class="c1"># Check file permissions</span>
ls<span class="w"> </span>-la<span class="w"> </span>/some/file.py
<span class="c1"># Option 1: Fix permissions</span>
chmod<span class="w"> </span>+r<span class="w"> </span>/some/file.py
<span class="c1"># Option 2: Skip problematic files</span>
cgc<span class="w"> </span>index<span class="w"> </span>.<span class="w"> </span>--ignore-errors
</code></pre></div></p>
<h4 id="issue-3-mcp-server-not-connecting"><strong>Issue 3: MCP server not connecting</strong></h4>
<p><strong>Symptoms:</strong>
- AI assistant says "CodeGraphContext tools not available"
- MCP server starts but IDE doesn't see it</p>
<p><strong>Solution:</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># 1. Verify server is running</span>
cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Should show "Server ready. Listening for requests..."</span>
<span class="c1"># 2. Check MCP configuration</span>
cat<span class="w"> </span>~/.config/cursor/mcp.json
<span class="c1"># Should contain "codegraphcontext" entry</span>
<span class="c1"># 3. Restart IDE completely</span>
<span class="c1"># Not just reload - full quit and reopen</span>
<span class="c1"># 4. Check IDE logs</span>
<span class="c1"># Cursor: Help > Toggle Developer Tools > Console</span>
<span class="c1"># Look for MCP connection errors</span>
<span class="c1"># 5. Test with manual MCP call</span>
<span class="nb">echo</span><span class="w"> </span><span class="s1">'{"method":"tools/list"}'</span><span class="w"> </span><span class="p">|</span><span class="w"> </span>cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Should return list of 18 tools</span>
</code></pre></div>
<h4 id="issue-4-slow-indexing-on-large-repositories"><strong>Issue 4: Slow indexing on large repositories</strong></h4>
<p><strong>Symptoms:</strong>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>index<span class="w"> </span>.
<span class="c1"># Takes > 5 minutes on 100k+ LOC repository</span>
</code></pre></div></p>
<p><strong>Solution:</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Option 1: Use Neo4j instead of FalkorDB</span>
cgc<span class="w"> </span>neo4j<span class="w"> </span>setup
cgc<span class="w"> </span>index<span class="w"> </span>.<span class="w"> </span>--db<span class="w"> </span>neo4j
<span class="c1"># Option 2: Exclude test files and dependencies</span>
cgc<span class="w"> </span>index<span class="w"> </span>.<span class="w"> </span>--exclude<span class="w"> </span><span class="s2">"tests/*"</span><span class="w"> </span>--exclude<span class="w"> </span><span class="s2">"node_modules/*"</span>
<span class="c1"># Option 3: Index in parallel</span>
cgc<span class="w"> </span>index<span class="w"> </span>.<span class="w"> </span>--parallel<span class="w"> </span><span class="m">4</span>
<span class="c1"># Option 4: Use pre-built bundle if available</span>
cgc<span class="w"> </span>load<span class="w"> </span><package-name>
</code></pre></div>
<h4 id="issue-5-graph-out-of-sync-with-code"><strong>Issue 5: Graph out of sync with code</strong></h4>
<p><strong>Symptoms:</strong>
- CGC shows old function names
- Missing new files</p>
<p><strong>Solution:</strong></p>
<div class="highlight"><pre><span></span><code><span class="c1"># Full reindex</span>
cgc<span class="w"> </span>reindex<span class="w"> </span>--force
<span class="c1"># Or use watch mode to auto-sync</span>
cgc<span class="w"> </span>watch<span class="w"> </span>.
</code></pre></div>
<h3 id="getting-help">Getting Help</h3>
<div class="highlight"><pre><span></span><code><span class="c1"># Built-in help</span>
cgc<span class="w"> </span><span class="nb">help</span>
cgc<span class="w"> </span><span class="nb">help</span><span class="w"> </span><command>
<span class="c1"># Check version</span>
cgc<span class="w"> </span>--version
<span class="c1"># Enable debug logging</span>
cgc<span class="w"> </span>--debug<span class="w"> </span>index<span class="w"> </span>.
<span class="c1"># Report issues</span>
<span class="c1"># GitHub: https://github.com/CodeGraphContext/CodeGraphContext/issues</span>
</code></pre></div>
<hr />
<h2 id="next-steps">Next Steps</h2>
<ul>
<li><strong>Learn by example</strong> → <a href="../user_journeys/">USER_JOURNEYS.md</a></li>
<li><strong>Detailed use cases</strong> → <a href="../use_cases_detailed/">USE_CASES_DETAILED.md</a></li>
<li><strong>Integration patterns</strong> → <a href="../integration_guide/">INTEGRATION_GUIDE.md</a></li>
<li><strong>CLI reference</strong> → <a href="../reference/cli_master/">CLI Reference</a></li>
<li><strong>MCP reference</strong> → <a href="../reference/mcp_master/">MCP Reference</a></li>
</ul>
<hr />
<h2 id="summary-quick-start-cheat-sheet">Summary: Quick Start Cheat Sheet</h2>
<h3 id="first-time-cli">First Time (CLI)</h3>
<div class="highlight"><pre><span></span><code>pip<span class="w"> </span>install<span class="w"> </span>codegraphcontext
<span class="nb">cd</span><span class="w"> </span>~/my-project
cgc<span class="w"> </span>index<span class="w"> </span>.
cgc<span class="w"> </span>stats
</code></pre></div>
<h3 id="first-time-mcp">First Time (MCP)</h3>
<div class="highlight"><pre><span></span><code>pip<span class="w"> </span>install<span class="w"> </span>codegraphcontext
<span class="nb">cd</span><span class="w"> </span>~/my-project
cgc<span class="w"> </span>index<span class="w"> </span>.
cgc<span class="w"> </span>mcp<span class="w"> </span>setup
cgc<span class="w"> </span>mcp<span class="w"> </span>start
<span class="c1"># Restart IDE</span>
</code></pre></div>
<h3 id="every-time-cli">Every Time (CLI)</h3>
<div class="highlight"><pre><span></span><code><span class="nb">cd</span><span class="w"> </span>~/my-project
cgc<span class="w"> </span>reindex<span class="w"> </span><span class="c1"># or cgc watch .</span>
cgc<span class="w"> </span>analyze<span class="w"> </span>callers<span class="w"> </span><<span class="k">function</span>>
</code></pre></div>
<h3 id="every-time-mcp">Every Time (MCP)</h3>
<div class="highlight"><pre><span></span><code>cgc<span class="w"> </span>mcp<span class="w"> </span>start<span class="w"> </span><span class="c1"># or auto-start</span>
<span class="c1"># Ask AI questions in natural language</span>
</code></pre></div>
<p><strong>That's it! You're ready to use CodeGraphContext.</strong> 🚀</p>
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