codegraph/README.md

<div align="center">

# CodeGraph

### Supercharge Claude Code, Cursor & Codex with Semantic Code Intelligence

**94% fewer tool calls · 77% faster exploration · 100% local**

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<br />

### Get Started

```bash
npx @colbymchenry/codegraph
```

<sub>Interactive installer auto-configures your agent(s) — Claude Code, Cursor, Codex CLI, opencode</sub>

#### Initialize Projects

```bash
cd your-project
codegraph init -i
```

![1_C_VYnhpys0UHrOuOgpgoyw](https://github.com/user-attachments/assets/f168182f-4d9a-44e0-94d7-08d018cc8a3a)

</div>

---

## 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**

| Codebase | With CG | Without CG | Improvement |
|----------|---------|------------|-------------|
| **VS Code** · TypeScript | 3 calls, 17s | 52 calls, 1m 37s | **94% fewer · 82% faster** |
| **Excalidraw** · TypeScript | 3 calls, 29s | 47 calls, 1m 45s | **94% fewer · 72% faster** |
| **Claude Code** · Python + Rust | 3 calls, 39s | 40 calls, 1m 8s | **93% fewer · 43% faster** |
| **Claude Code** · Java | 1 call, 19s | 26 calls, 1m 22s | **96% fewer · 77% faster** |
| **Alamofire** · Swift | 3 calls, 22s | 32 calls, 1m 39s | **91% fewer · 78% faster** |
| **Swift Compiler** · Swift/C++ | 6 calls, 35s | 37 calls, 2m 8s | **84% fewer · 73% faster** |

<details>
<summary><strong>Full benchmark details</strong></summary>

All tests used Claude Opus 4.6 (1M context) with Claude Code v2.1.91. Each test spawned a single Explore agent with the same question.

**Queries used:**
| Codebase | Query |
|----------|-------|
| VS Code | "How does the extension host communicate with the main process?" |
| Excalidraw | "How does collaborative editing and real-time sync work?" |
| Claude Code (Python+Rust) | "How does tool execution work end to end?" |
| Claude Code (Java) | "How does tool execution work end to end?" |
| Alamofire | "Trace how a request flows from Session.request() through to the URLSession layer" |
| Swift Compiler | "How does the Swift compiler handle error diagnostics?" |

**With CodeGraph — the agent uses `codegraph_explore` and stops:**
| Codebase | Files Indexed | Nodes | Tool Uses | Tokens | Time | File Reads |
|----------|--------------|-------|-----------|--------|------|------------|
| VS Code (TypeScript) | 4,002 | 59,377 | 3 | 56.6k | 17s | 0 |
| Excalidraw (TypeScript) | 626 | 9,859 | 3 | 57.1k | 29s | 0 |
| Claude Code (Python+Rust) | 115 | 3,080 | 3 | 67.1k | 39s | 0 |
| Claude Code (Java) | — | — | 1 | 40.8k | 19s | 0 |
| Alamofire (Swift) | 102 | 2,624 | 3 | 57.3k | 22s | 0 |
| Swift Compiler (Swift/C++) | 25,874 | 272,898 | 6 | 77.4k | 35s | 0 |

**Without CodeGraph — the agent uses grep, find, ls, and Read extensively:**
| Codebase | Tool Uses | Tokens | Time | File Reads |
|----------|-----------|--------|------|------------|
| VS Code (TypeScript) | 52 | 89.4k | 1m 37s | ~15 |
| Excalidraw (TypeScript) | 47 | 77.9k | 1m 45s | ~20 |
| Claude Code (Python+Rust) | 40 | 69.3k | 1m 8s | ~15 |
| Claude Code (Java) | 26 | 73.3k | 1m 22s | ~15 |
| Alamofire (Swift) | 32 | 52.4k | 1m 39s | ~10 |
| Swift Compiler (Swift/C++) | 37 | 99.1k | 2m 8s | ~20 |

**Key observations:**
- With CodeGraph, the agent **never fell back to reading files** — it trusted the codegraph_explore results completely
- Without CodeGraph, agents spent most of their time on discovery (find, ls, grep) before they could even start reading relevant code
- The Java codebase needed only **1 codegraph_explore call** to answer the entire question
- Cross-language queries (Python+Rust) worked seamlessly — CodeGraph's graph traversal found connections across language boundaries
- The Swift benchmark (Alamofire) traced a **9-step call chain** from `Session.request()` to `URLSession.dataTask()` — CodeGraph's graph traversal at depth 3 captured the full chain in one explore call
- The **Swift Compiler** benchmark is the largest codebase tested (**25,874 files, 272,898 nodes**) — CodeGraph indexed it in under 4 minutes and the agent answered a complex cross-cutting question with **6 explore calls and zero file reads** in 35 seconds

</details>

---

## Key Features

| | |
|---|---|
| **Smart Context Building** | One tool call returns entry points, related symbols, and code snippets — no expensive exploration agents |
| **Full-Text Search** | Find code by name instantly across your entire codebase, powered by FTS5 |
| **Impact Analysis** | Trace callers, callees, and the full impact radius of any symbol before making changes |
| **Always Fresh** | File watcher uses native OS events (FSEvents/inotify/ReadDirectoryChangesW) with debounced auto-sync — the graph stays current as you code, zero config |
| **19+ Languages** | TypeScript, JavaScript, Python, Go, Rust, Java, C#, PHP, Ruby, C, C++, Swift, Kotlin, Dart, Svelte, Liquid, Pascal/Delphi |
| **Framework-aware Routes** | Recognizes web-framework routing files and links URL patterns to their handlers across 13 frameworks |
| **100% Local** | No data leaves your machine. No API keys. No external services. SQLite database only |

---

## 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.

| Framework | Shapes recognized |
|---|---|
| **Django** | `path()`, `re_path()`, `url()`, `include()` in `urls.py` (CBV `.as_view()`, dotted paths) |
| **Flask** | `@app.route('/path', methods=[...])`, blueprint routes |
| **FastAPI** | `@app.get(...)`, `@router.post(...)`, all standard methods |
| **Express** | `app.get(...)`, `router.post(...)` with middleware chains |
| **Laravel** | `Route::get()`, `Route::resource()`, `Controller@action`, tuple syntax |
| **Rails** | `get '/x', to: 'users#index'`, hash-rocket `=>` syntax |
| **Spring** | `@GetMapping`, `@PostMapping`, `@RequestMapping` on methods |
| **Gin / chi / gorilla / mux** | `r.GET(...)`, `router.HandleFunc(...)` |
| **Axum / actix / Rocket** | `.route("/x", get(handler))` |
| **ASP.NET** | `[HttpGet("/x")]` attributes on action methods |
| **Vapor** | `app.get("x", use: handler)` |
| **React Router** / **SvelteKit** | Route component nodes |

---

## Quick Start

### 1. Run the Installer

```bash
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):**

```bash
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
```

| Flag | Values | Default |
|---|---|---|
| `--target` | `auto`, `all`, `none`, or csv (`claude,cursor,...`) | prompt |
| `--location` | `global`, `local` | prompt |
| `--yes` | (boolean) | prompt every step |
| `--no-permissions` | (boolean) skip Claude auto-allow list | permissions on |
| `--print-config <id>` | dump snippet for one agent and exit | — |

### 2. Restart Your Agent

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

### 3. Initialize Projects

```bash
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.

<details>
<summary><strong>Manual Setup (Alternative)</strong></summary>

**Install globally:**
```bash
npm install -g @colbymchenry/codegraph
```

**Add to `~/.claude.json`:**
```json
{
  "mcpServers": {
    "codegraph": {
      "type": "stdio",
      "command": "codegraph",
      "args": ["serve", "--mcp"]
    }
  }
}
```

**Add to `~/.claude/settings.json` (optional, for auto-allow):**
```json
{
  "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"
    ]
  }
}
```

</details>

<details>
<summary><strong>Global Instructions Reference</strong></summary>

The installer automatically adds these instructions to `~/.claude/CLAUDE.md`:

```markdown
## 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?"
```

</details>

---

## 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](https://tree-sitter.github.io/) 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

```bash
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.

```bash
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
```

| Option | Description | Default |
|--------|-------------|---------|
| `--stdin` | Read file list from stdin | `false` |
| `-d, --depth <n>` | Max dependency traversal depth | `5` |
| `-f, --filter <glob>` | Custom glob to identify test files | auto-detect |
| `-j, --json` | Output as JSON | `false` |
| `-q, --quiet` | Output file paths only | `false` |

**CI/hook example:**

```bash
#!/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:

| Tool | Purpose |
|------|---------|
| `codegraph_search` | Find symbols by name across the codebase |
| `codegraph_context` | Build relevant code context for a task |
| `codegraph_callers` | Find what calls a function |
| `codegraph_callees` | Find what a function calls |
| `codegraph_impact` | Analyze what code is affected by changing a symbol |
| `codegraph_node` | Get details about a specific symbol (optionally with source code) |
| `codegraph_files` | Get indexed file structure (faster than filesystem scanning) |
| `codegraph_status` | Check index health and statistics |

---

## Library Usage

```typescript
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:

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

| Option | Description | Default |
|--------|-------------|---------|
| `languages` | Languages to index (auto-detected if empty) | `[]` |
| `exclude` | Glob patterns to ignore | `["node_modules/**", ...]` |
| `frameworks` | Framework hints for better resolution | `[]` |
| `maxFileSize` | Skip files larger than this (bytes) | `1048576` (1MB) |
| `extractDocstrings` | Extract docstrings from code | `true` |
| `trackCallSites` | Track call site locations | `true` |

## Supported Languages

| Language | Extension | Status |
|----------|-----------|--------|
| TypeScript | `.ts`, `.tsx` | Full support |
| JavaScript | `.js`, `.jsx`, `.mjs` | Full support |
| Python | `.py` | Full support |
| Go | `.go` | Full support |
| Rust | `.rs` | Full support |
| Java | `.java` | Full support |
| C# | `.cs` | Full support |
| PHP | `.php` | Full support |
| Ruby | `.rb` | Full support |
| C | `.c`, `.h` | Full support |
| C++ | `.cpp`, `.hpp`, `.cc` | Full support |
| Swift | `.swift` | Full support |
| Kotlin | `.kt`, `.kts` | Full support |
| Scala | `.scala`, `.sc` | Full support (classes, traits, methods, type aliases, Scala 3 enums) |
| Dart | `.dart` | Full support |
| Svelte | `.svelte` | Full support (script extraction, Svelte 5 runes, SvelteKit routes) |
| Vue | `.vue` | Full support (script + script-setup extraction, Nuxt page/API/middleware routes) |
| Liquid | `.liquid` | Full support |
| Pascal / Delphi | `.pas`, `.dpr`, `.dpk`, `.lpr` | Full support (classes, records, interfaces, enums, DFM/FMX form files) |

## 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:

  ```bash
  # 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

---

<div align="center">

**Made for the Claude Code community**

[Report Bug](https://github.com/colbymchenry/codegraph/issues) · [Request Feature](https://github.com/colbymchenry/codegraph/issues)

</div>