codebase-synapse MCP server

🧠 Codebase Synapse

Give your AI agent a deep understanding of your entire codebase.

An MCP server that indexes your codebase into a local knowledge graph with 52 AI tools — semantic search, call-graph traversal, git archaeology, blast-radius analysis, and more.

Works with Claude Code · Cursor · Windsurf · Zed · Any MCP client

The Problem

AI coding agents (Claude, Cursor, etc.) are powerful — but they work with limited context. They can only see the files you open or feed them. Ask about call chains, architectural patterns, or blast-radius impact, and they guess.

Codebase Synapse fixes this. It indexes your entire repo into a local knowledge graph stored in SQLite, giving your AI agent real answers backed by structural analysis — not hallucinations.

How it works

graph LR
    A["📁 Your Codebase"] -->|Tree-sitter| B["🧩 Parser"]
    B -->|Symbols & Edges| C["🕸️ Knowledge Graph"]
    C -->|SQLite| D["💾 Local DB"]
    D -->|52 MCP Tools| E["🤖 AI Agent"]
    
    style A fill:#1a1b26,stroke:#7aa2f7,color:#c0caf5
    style B fill:#1a1b26,stroke:#bb9af7,color:#c0caf5
    style C fill:#1a1b26,stroke:#9ece6a,color:#c0caf5
    style D fill:#1a1b26,stroke:#e0af68,color:#c0caf5
    style E fill:#1a1b26,stroke:#f7768e,color:#c0caf5

⚡ Quick Start

1. Index your project (CLI, Zoekt-style)

codebase-synapse index /path/to/your/repo

Indexing runs as a separate CLI command and writes into ~/.codebase-synapse/codebase.db. The first index is the slow one; re-running it only re-indexes changed files. The MCP server never indexes — it only reads the pre-built index.

2. Start the MCP server

npx codebase-synapse

That's it. No Docker. No database setup. No cloud. The server starts via stdio and serves the pre-built index to your MCP client.

Configure your client

Claude Code / Claude Desktop

Add to your claudedesktopconfig.json or mcp_servers.json:

{
  "mcpServers": {
    "codebase-synapse": {
      "command": "npx",
      "args": ["-y", "codebase-synapse"]
    }
  }
}

Cursor

Add to your .cursor/mcp.json:

{
  "mcpServers": {
    "codebase-synapse": {
      "command": "npx",
      "args": ["-y", "codebase-synapse"]
    }
  }
}

Other MCP clients

Any MCP client that supports stdio transport works. Just point it at:

npx -y codebase-synapse

✨ What It Does

🔍 Search & Discovery

Shortened. The full README is on GitHub.