cli-reference.md

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:

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.

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	Delete every project from the shared graph and clear the selected repository's sync cache. With --update-graph, rebuild after deletion.
--batch-size	Override Memgraph flush batch size
--orchestrator	Specify provider:model for main operations (e.g., google:gemini-2.5-pro, ollama:llama3.2)
--cypher	Specify provider:model for graph queries (e.g., google:gemini-2.5-flash, ollama:codellama)
-o, --output	Write the updated graph to a JSON path. Requires --update-graph.

cgr export

Export the knowledge graph to JSON.

cgr export -o my_graph.json

cgr optimize

AI-powered codebase optimisation.

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.

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.

cgr mcp-server

cgr index

Index a repository to protobuf for offline use.

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

cgr doctor

Check that all required dependencies and services are available.

cgr doctor

cgr language

Manage language support.

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