---
description: "Complete CLI reference for Code-Graph-RAG commands and Makefile targets."
---

# CLI Reference

The `cgr` command is the main entry point for Code-Graph-RAG.

## Built-in Help

List commands by workflow or show the detailed page for a command:

```bash
cgr help
cgr help start
cgr help daemon logs
```

`cgr COMMAND --help` displays the same command-specific information.

## Core Commands

### `cgr start`

Parse a repository and/or start the interactive query CLI.

```bash
cgr start --repo-path /path/to/repo [OPTIONS]
```

| Option | Description |
|--------|-------------|
| `--repo-path` | Path to repository (defaults to current directory) |
| `--update-graph` | Parse and ingest the repository into the knowledge graph |
| `--clean` | **Destructive.** Delete every project from the shared graph and clear the selected repository's sync cache. With `--update-graph`, rebuild after deletion. Asks for confirmation when other projects would be destroyed. |
| `-y`, `--yes` | Answer yes to destructive confirmations, such as the one `--clean` asks. Required when `--clean` runs non-interactively and other projects would be destroyed, or when the existing projects cannot be listed. |
| `--batch-size` | Override Memgraph flush batch size |
| `--orchestrator` | Specify provider:model for main operations (e.g., `anthropic:claude-sonnet-5`, `google:gemini-3.6-flash`, `ollama:qwen2.5-coder`) |
| `--cypher` | Specify provider:model for graph queries (e.g., `anthropic:claude-sonnet-5`, `google:gemini-3.5-flash-lite`, `ollama:qwen2.5-coder`) |
| `-o`, `--output` | Write the updated graph to a JSON path. Requires `--update-graph`. |

### `cgr export`

Export the knowledge graph to JSON.

```bash
cgr export -o my_graph.json
```

### `cgr optimize`

AI-powered codebase optimisation.

```bash
cgr optimize <language> --repo-path /path/to/repo [OPTIONS]
```

| Option | Description |
|--------|-------------|
| `--repo-path` | Path to repository |
| `--orchestrator` | Specify provider:model for operations |
| `--batch-size` | Override Memgraph flush batch size |
| `--reference-document` | Path to reference documentation for guided optimisation |

Supported languages: `python`, `javascript`, `typescript`, `rust`, `go`, `java`, `scala`, `c`, `cpp`

### `cgr dead-code`

Report functions and methods unreachable from any entry point (candidates for
review, not a guaranteed delete list). See [Dead Code Detection](dead-code.md).

```bash
cgr dead-code [OPTIONS]
```

| Option | Description |
|--------|-------------|
| `--project-name`, `-n` | Project to scan. Defaults to the sole indexed project. |
| `--entry-point`, `-e` | Treat symbols whose qualified name ends with this value as reachable roots. Repeatable. |
| `--decorator-root` | Treat symbols carrying this decorator as roots. Repeatable. |
| `--exclude` | Glob matched against a symbol's file path to exclude. Repeatable. |
| `--include-tests` / `--no-include-tests` | Treat test code as reachable roots. On by default. |
| `--classes` / `--no-classes` | Also report unreachable classes. Off by default. |
| `--format` | Output format: `table` (default) or `json`. |
| `--output`, `-o` | Write the report to a file instead of stdout. |
| `--fail-on-found` | Exit with code 1 when any candidate is found (useful in CI). |

### `cgr mcp-server`

Serve cgr tools to MCP clients over stdio or HTTP.

```bash
cgr mcp-server
```

### `cgr index`

Index a repository to protobuf for offline use.

```bash
cgr index -o ./index-output --repo-path ./my-project
```

### `cgr doctor`

Check that all required dependencies and services are available.

```bash
cgr doctor
```

### `cgr language`

Manage language support.

```bash
cgr language add-grammar <language-name>
cgr language add-grammar --grammar-url <url>
cgr language list-languages
cgr language remove-language <language-name>
```

## Makefile Commands

| Command | Description |
|---------|-------------|
| `make help` | Show help message |
| `make all` | Install everything for full development environment |
| `make install` | Install project dependencies with full language support |
| `make python` | Install project dependencies for Python only |
| `make dev` | Setup development environment (install deps + pre-commit hooks) |
| `make test` | Run unit tests only (fast, no Docker) |
| `make test-parallel` | Run unit tests in parallel (fast, no Docker) |
| `make test-integration` | Run integration tests (requires Docker) |
| `make test-all` | Run all tests including integration and e2e (requires Docker) |
| `make test-parallel-all` | Run all tests in parallel (requires Docker) |
| `make clean` | Clean up build artifacts and cache |
| `make build-grammars` | Build grammar submodules |
| `make watch` | Watch repository for changes and update graph in real-time |
| `make readme` | Regenerate README.md from codebase |
| `make lint` | Run ruff check |
| `make format` | Run ruff format |
| `make typecheck` | Run type checking with ty |
| `make check` | Run all checks: lint, typecheck, test |
| `make pre-commit` | Run all pre-commit checks locally |