CodeGraph

npx @colbymchenry/codegraph

cd your-project
codegraph init -i

Why CodeGraph?

When Claude Code explores a codebase, it spawns Explore agents that scan files with grep, glob, and Read — consuming tokens on every tool call.

CodeGraph gives those agents a pre-indexed knowledge graph — symbol relationships, call graphs, and code structure. Agents query the graph instantly instead of scanning files.

Benchmark Results

Tested across 6 real-world codebases comparing Claude Code's Explore agent with and without CodeGraph:

Average: 92% fewer tool calls · 71% faster

Key Features

Framework-aware Routes

CodeGraph detects web-framework routing files and emits route nodes linked by references edges to their handler classes or functions. Querying callers of a view/controller now surfaces the URL pattern that binds it.

Quick Start

1. Run the Installer

npx @colbymchenry/codegraph

The installer will:

• Ask which agent(s) to configure — auto-detects installed ones from: Claude Code, Cursor, Codex CLI, opencode
• Prompt to install codegraph on your PATH (so agents can launch the MCP server)
• Ask whether configs apply to all your projects or just this one
• Write each chosen agent's MCP server config + an instructions file (e.g. CLAUDE.md, .cursor/rules/codegraph.mdc, ~/.codex/AGENTS.md)
• Set up auto-allow permissions when Claude Code is one of the targets
• Initialize your current project (local installs only)

Non-interactive (scripting / CI):

codegraph install --yes                              # auto-detect agents, install global
codegraph install --target=cursor,claude --yes       # explicit target list
codegraph install --target=auto --location=local     # detected agents, project-local
codegraph install --print-config codex               # print snippet, no file writes

2. Restart Your Agent

Restart your agent (Claude Code / Cursor / Codex CLI / opencode) for the MCP server to load.

3. Initialize Projects

cd your-project
codegraph init -i

Builds the per-project knowledge graph index. Also wires up any project-local agent surfaces (e.g. Cursor's .cursor/rules/codegraph.mdc) so a single global codegraph install works in every project you open — no need to re-run the installer per project.

That's it — your agent will use CodeGraph tools automatically when a .codegraph/ directory exists.

npm install -g @colbymchenry/codegraph

{
  "mcpServers": {
    "codegraph": {
      "type": "stdio",
      "command": "codegraph",
      "args": ["serve", "--mcp"]
    }
  }
}

{
  "permissions": {
    "allow": [
      "mcp__codegraph__codegraph_search",
      "mcp__codegraph__codegraph_context",
      "mcp__codegraph__codegraph_callers",
      "mcp__codegraph__codegraph_callees",
      "mcp__codegraph__codegraph_impact",
      "mcp__codegraph__codegraph_node",
      "mcp__codegraph__codegraph_status",
      "mcp__codegraph__codegraph_files"
    ]
  }
}

## CodeGraph

CodeGraph builds a semantic knowledge graph of codebases for faster, smarter code exploration.

### If `.codegraph/` exists in the project

**NEVER call `codegraph_explore` or `codegraph_context` directly in the main session.** These tools return large amounts of source code that fills up main session context. Instead, ALWAYS spawn an Explore agent for any exploration question (e.g., "how does X work?", "explain the Y system", "where is Z implemented?").

**When spawning Explore agents**, include this instruction in the prompt:

> This project has CodeGraph initialized (.codegraph/ exists). Use `codegraph_explore` as your PRIMARY tool — it returns full source code sections from all relevant files in one call.
>
> **Rules:**
> 1. Follow the explore call budget in the `codegraph_explore` tool description — it scales automatically based on project size.
> 2. Do NOT re-read files that codegraph_explore already returned source code for. The source sections are complete and authoritative.
> 3. Only fall back to grep/glob/read for files listed under "Additional relevant files" if you need more detail, or if codegraph returned no results.

**The main session may only use these lightweight tools directly** (for targeted lookups before making edits, not for exploration):

| Tool | Use For |
|------|---------|
| `codegraph_search` | Find symbols by name |
| `codegraph_callers` / `codegraph_callees` | Trace call flow |
| `codegraph_impact` | Check what's affected before editing |
| `codegraph_node` | Get a single symbol's details |

### If `.codegraph/` does NOT exist

At the start of a session, ask the user if they'd like to initialize CodeGraph:

"I notice this project doesn't have CodeGraph initialized. Would you like me to run `codegraph init -i` to build a code knowledge graph?"

How It Works

┌─────────────────────────────────────────────────────────────────┐
│                        Claude Code                               │
│                                                                  │
│  "Implement user authentication"                                 │
│           │                                                      │
│           ▼                                                      │
│  ┌─────────────────┐      ┌─────────────────┐                   │
│  │  Explore Agent  │ ──── │  Explore Agent  │                   │
│  └────────┬────────┘      └────────┬────────┘                   │
│           │                        │                             │
└───────────┼────────────────────────┼─────────────────────────────┘
            │                        │
            ▼                        ▼
┌───────────────────────────────────────────────────────────────────┐
│                     CodeGraph MCP Server                          │
│  ┌─────────────┐  ┌─────────────┐  ┌─────────────┐               │
│  │   Search    │  │   Callers   │  │   Context   │               │
│  │  "auth"     │  │  "login()"  │  │  for task   │               │
│  └──────┬──────┘  └──────┬──────┘  └──────┬──────┘               │
│         │                │                │                       │
│         └────────────────┼────────────────┘                       │
│                          ▼                                        │
│              ┌───────────────────────┐                            │
│              │   SQLite Graph DB     │                            │
│              │   • 387 symbols       │                            │
│              │   • 1,204 edges       │                            │
│              │   • Instant lookups   │                            │
│              └───────────────────────┘                            │
└───────────────────────────────────────────────────────────────────┘

1. Extraction — tree-sitter parses source code into ASTs. Language-specific queries extract nodes (functions, classes, methods) and edges (calls, imports, extends, implements).

2. Storage — Everything goes into a local SQLite database (.codegraph/codegraph.db) with FTS5 full-text search.

3. Resolution — After extraction, references are resolved: function calls → definitions, imports → source files, class inheritance, and framework-specific patterns.

4. Auto-Sync — The MCP server watches your project using native OS file events. Changes are debounced (2-second quiet window), filtered to source files only, and incrementally synced. The graph stays fresh as you code — no configuration needed.

CLI Reference

codegraph                         # Run interactive installer
codegraph install                 # Run installer (explicit)
codegraph init [path]             # Initialize in a project (--index to also index)
codegraph uninit [path]           # Remove CodeGraph from a project (--force to skip prompt)
codegraph index [path]            # Full index (--force to re-index, --quiet for less output)
codegraph sync [path]             # Incremental update
codegraph status [path]           # Show statistics
codegraph query <search>          # Search symbols (--kind, --limit, --json)
codegraph files [path]            # Show file structure (--format, --filter, --max-depth, --json)
codegraph context <task>          # Build context for AI (--format, --max-nodes)
codegraph affected [files...]     # Find test files affected by changes (see below)
codegraph serve --mcp             # Start MCP server

codegraph affected

Traces import dependencies transitively to find which test files are affected by changed source files.

codegraph affected src/utils.ts src/api.ts         # Pass files as arguments
git diff --name-only | codegraph affected --stdin   # Pipe from git diff
codegraph affected src/auth.ts --filter "e2e/*"     # Custom test file pattern

CI/hook example:

#!/usr/bin/env bash
AFFECTED=$(git diff --name-only HEAD | codegraph affected --stdin --quiet)
if [ -n "$AFFECTED" ]; then
  npx vitest run $AFFECTED
fi

MCP Tools

When running as an MCP server, CodeGraph exposes these tools to Claude Code:

Library Usage

import CodeGraph from '@colbymchenry/codegraph';

const cg = await CodeGraph.init('/path/to/project');
// Or: const cg = await CodeGraph.open('/path/to/project');

await cg.indexAll({
  onProgress: (p) => console.log(`${p.phase}: ${p.current}/${p.total}`)
});

const results = cg.searchNodes('UserService');
const callers = cg.getCallers(results[0].node.id);
const context = await cg.buildContext('fix login bug', { maxNodes: 20, includeCode: true, format: 'markdown' });
const impact = cg.getImpactRadius(results[0].node.id, 2);

cg.watch();   // auto-sync on file changes
cg.unwatch(); // stop watching
cg.close();

Configuration

The .codegraph/config.json file controls indexing:

{
  "version": 1,
  "languages": ["typescript", "javascript"],
  "exclude": ["node_modules/**", "dist/**", "build/**", "*.min.js"],
  "frameworks": [],
  "maxFileSize": 1048576,
  "extractDocstrings": true,
  "trackCallSites": true
}

Supported Languages

Troubleshooting

"CodeGraph not initialized" — Run codegraph init in your project directory first.

Indexing is slow — Check that node_modules and other large directories are excluded. Use --quiet to reduce output overhead.

Indexing is slow / MCP database is locked / WASM fallback active — codegraph ships with a WASM SQLite fallback for environments where better-sqlite3 (a native module, declared as optionalDependencies) can't install. The fallback is 5-10x slower than the native backend and uses a journal mode that lets writers block readers, so MCP queries can also hit database is locked while indexing runs. Run codegraph status and look at the Backend: line:

• Backend: native — you're on the fast path, nothing to do.

• Backend: wasm — you're on the slow fallback. Common causes: missing C build tools, prebuilt binary unavailable for your Node version, or your Node version changed after install. Fix:

  # macOS
  xcode-select --install                                  # installs the C compiler
  
  # Linux (Debian / Ubuntu)
  sudo apt install build-essential python3 make
  
  # Linux (RHEL / Fedora)
  sudo yum groupinstall "Development Tools"
  
  # Then rebuild on any platform:
  npm rebuild better-sqlite3
  
  # Or force-include as a hard dep:
  npm install better-sqlite3 --save

  After the fix, codegraph status should show Backend: native.

MCP server not connecting — Ensure the project is initialized/indexed, verify the path in your MCP config, and check that codegraph serve --mcp works from the command line.

Missing symbols — The MCP server auto-syncs on save (wait a couple seconds). Run codegraph sync manually if needed. Check that the file's language is supported and isn't excluded by config patterns.

License

MIT