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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 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.

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 duplicates

Report groups of structurally duplicated functions and methods (copy-pastes, including renamed and lightly edited copies). See Duplicate Code Detection.

cgr duplicates [OPTIONS]
Option Description
--project-name, -n Project to scan. Defaults to the sole indexed project.
--threshold Minimum similarity for a near-duplicate pair, 0-1. Default 0.8.
--min-size Minimum skeleton size (tree nodes) for a function to be considered. Default 15.
--exact-only Report only identical-fingerprint clone groups; skip similarity scoring.
--exclude Glob matched against a symbol's file path to exclude. Repeatable.
--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 duplicate 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