MCP Server (Claude Code Integration)

Code-Graph-RAG can run as an MCP (Model Context Protocol) server, enabling seamless integration with Claude Code and other MCP clients.

Quick Setup

If installed via pip (and code-graph-rag is on your PATH):

claude mcp add --transport stdio code-graph-rag \
  --env TARGET_REPO_PATH=/absolute/path/to/your/project \
  --env CYPHER_PROVIDER=openai \
  --env CYPHER_MODEL=gpt-4 \
  --env CYPHER_API_KEY=your-api-key \
  -- code-graph-rag mcp-server

If installed from source:

claude mcp add --transport stdio code-graph-rag \
  --env TARGET_REPO_PATH=/absolute/path/to/your/project \
  --env CYPHER_PROVIDER=openai \
  --env CYPHER_MODEL=gpt-4 \
  --env CYPHER_API_KEY=your-api-key \
  -- uv run --directory /path/to/code-graph-rag code-graph-rag mcp-server

Using Current Directory

cd /path/to/your/project

claude mcp add --transport stdio code-graph-rag \
  --env TARGET_REPO_PATH="$(pwd)" \
  --env CYPHER_PROVIDER=google \
  --env CYPHER_MODEL=gemini-2.0-flash \
  --env CYPHER_API_KEY=your-google-api-key \
  -- uv run --directory /absolute/path/to/code-graph-rag code-graph-rag mcp-server

Prerequisites

git clone https://github.com/vitali87/code-graph-rag.git
cd code-graph-rag
uv sync

cgr daemon up

Available Tools

Tool	Description
list_projects	List all indexed projects in the knowledge graph database. Returns a list of project names that have been indexed.
delete_project	Delete a specific project from the knowledge graph database. This removes all nodes associated with the project while preserving other projects. Use list_projects first to see available projects.
wipe_database	WARNING: Completely wipe the entire database, removing ALL indexed projects. This cannot be undone. Use delete_project for removing individual projects.
index_repository	WARNING: Clears all data for the current project including its embeddings. Parse and ingest the repository into the Memgraph knowledge graph. Use update_repository for incremental updates. Only use when explicitly requested.
update_repository	Update the repository in the Memgraph knowledge graph without clearing existing data. Use this for incremental updates.
query_code_graph	Query the codebase knowledge graph using natural language. Use semantic_search unless you know the exact names of classes/functions you are searching for. Ask questions like 'What functions call UserService.create_user?' or 'Show me all classes that implement the Repository interface'.
get_code_snippet	Retrieve source code for a function, class, or method by its qualified name. Returns the source code, file path, line numbers, and docstring.
surgical_replace_code	Surgically replace an exact code block in a file using diff-match-patch. Only modifies the exact target block, leaving the rest unchanged.
read_file	Read the contents of a file from the project. Supports pagination for large files.
write_file	Write content to a file, creating it if it doesn't exist.
list_directory	List contents of a directory in the project.
semantic_search	Performs a semantic search for functions based on a natural language query describing their purpose, returning a list of potential matches with similarity scores. Requires the 'semantic' extra to be installed.
structural_search	Search code structurally by AST pattern using ast-grep syntax (not text/regex). Returns file paths, line and column numbers, and the matched code. Requires the 'ast-grep' extra to be installed.
structural_replace	Rewrite code structurally by AST pattern using ast-grep syntax. Metavariables captured by the pattern are substituted into the rewrite. Defaults to dry_run (returns a diff); set dry_run=false to write changes. Requires the 'ast-grep' extra to be installed.
ask_agent	Ask the Code Graph RAG agent a question about the codebase. Uses the full RAG pipeline to analyse the code graph and provide a detailed answer. Use this for general questions about architecture, functionality, and code relationships.

Example Usage

> Index this repository
> What functions call UserService.create_user?
> Update the login function to add rate limiting

LLM Provider Options

=== "OpenAI"

```bash
--env CYPHER_PROVIDER=openai \
--env CYPHER_MODEL=gpt-4 \
--env CYPHER_API_KEY=sk-...
```

=== "Google Gemini"

```bash
--env CYPHER_PROVIDER=google \
--env CYPHER_MODEL=gemini-2.5-flash \
--env CYPHER_API_KEY=...
```

=== "Ollama (free, local)"

```bash
--env CYPHER_PROVIDER=ollama \
--env CYPHER_MODEL=llama3.2
```

Multi-Repository Setup

Add separate named instances for different projects:

claude mcp add --transport stdio code-graph-rag-backend \
  --env TARGET_REPO_PATH=/path/to/backend \
  --env CYPHER_PROVIDER=openai \
  --env CYPHER_MODEL=gpt-4 \
  --env CYPHER_API_KEY=your-api-key \
  -- uv run --directory /path/to/code-graph-rag code-graph-rag mcp-server

claude mcp add --transport stdio code-graph-rag-frontend \
  --env TARGET_REPO_PATH=/path/to/frontend \
  --env CYPHER_PROVIDER=openai \
  --env CYPHER_MODEL=gpt-4 \
  --env CYPHER_API_KEY=your-api-key \
  -- uv run --directory /path/to/code-graph-rag code-graph-rag mcp-server

!!! warning Only one repository can be indexed at a time per MCP instance. When you index a new repository, the previous repository's data is automatically cleared.

Troubleshooting

Issue	Solution
Can't find uv/code-graph-rag	Use absolute paths from which uv
Wrong repository analysed	Set TARGET_REPO_PATH to an absolute path
Memgraph connection failed	Ensure docker ps shows Memgraph running
Tools not showing	Run claude mcp list to verify installation

Remove

claude mcp remove code-graph-rag