Codebase Synapse README | AllMCPs

🧠 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.

Codebase Synapse — Knowledge graph visualization

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.

Codebase Synapse demo — indexing and impact analysis

How it works

mermaid

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)

bash

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

Terminal

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 claude_desktop_config.json or mcp_servers.json:

config.json

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

Cursor

Add to your .cursor/mcp.json:

config.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:

Terminal

npx -y codebase-synapse

✨ What It Does

🔍 Search & Discovery

Tool	Description
`semantic_search`	Vector similarity search using local embeddings (all-MiniLM-L6-v2)
`search_code`	Full-text search across code (FTS5 + BM25 ranking)
`search_symbol`	Find functions, classes, types by name or pattern
`hybrid_search`	Combined semantic + lexical search with RRF fusion
`find_similar`	Find structurally similar code using MinHash + LSH
`find_symbol_everywhere`	Locate a symbol across all indexed projects

🕸️ Knowledge Graph

Tool	Description
`get_callers` / `get_callees`	Navigate the call graph in either direction
`get_imports` / `get_dependents`	Trace dependency chains
`impact_analysis`	Compute blast radius before editing a file
`find_path`	Find the shortest connection between two symbols
`find_dead_code`	Detect unreachable functions and unused exports
`get_pagerank`	Identify the most critical nodes in your architecture
`query_graph`	Run Cypher-like queries against the knowledge graph

🏗️ Architecture

Tool	Description
`get_architecture`	Full project architecture overview (languages, entry points, hotspots)
`get_file_structure`	Directory tree with symbol annotations
`project_overview`	High-level summary with key metrics
`get_route_map`	Extract HTTP routes and their handler mappings
`suggest_boundaries`	Detect module boundaries via Leiden clustering
`check_boundaries`	Validate cross-module dependencies against defined boundaries
`get_clusters`	Community detection across the codebase

🔬 Git Archaeology

Tool	Description
`git_archaeology`	Deep history analysis of a file (authors, churn, evolution)
`get_hotspots`	Files with highest complexity × change frequency
`detect_change_coupling`	Files that always change together
`get_recent_semantic_changes`	Semantically meaningful recent changes
`index_git_history`	Build temporal analysis from git log

🧠 Memory & Context

Tool	Description
`memory_store` / `memory_search` / `memory_list`	Persistent notes, facts, and decisions across sessions
`session_remember` / `session_recall`	Short-term memory within a session
`get_context`	Budgeted context preparation for AI agents
`get_edit_context`	Focused context for a specific file edit
`get_working_set`	Recently accessed and modified files
`manage_adr`	Architecture Decision Records management

🛡️ Codebase Guard

Included as a bonus: codebase-guard is a PreToolUse hook for Claude Code that blocks writes to high-impact files until the agent runs impact_analysis first.

It uses PageRank scores and blast-radius data from the knowledge graph to identify architectural hubs. No more accidental edits to core files.

🔧 Technical Details


Language	Rust (compiled native binary)
Transport	MCP stdio (JSON-RPC)
Storage	SQLite (WAL mode, zero config)
Embeddings	all-MiniLM-L6-v2 via Candle (offline, local, lazy-loaded)
Parsing	Tree-sitter (10 languages)
Distribution	npm with prebuilt binaries (Windows, macOS, Linux × x64, arm64)

Supported Languages

Rust · Python · TypeScript · JavaScript · Go · Java · C# · PHP · C · C++

Architecture

Code

src/
├── parser/       # Tree-sitter parsing & entity extraction
├── graph/        # Knowledge graph, PageRank, Leiden clustering
├── indexer/      # Repository indexing pipeline
├── search/       # BM25 full-text + vector cosine + hybrid RRF
├── embedding/    # Candle-based local embeddings (feature-gated)
├── memory/       # Persistent & session memory stores
├── mcp/          # MCP protocol transport + 52 tool handlers
├── git/          # Git archaeology, intent classification, hotspots
├── context/      # Budgeted context preparation for AI
├── cypher/       # Nom-based Cypher parser → SQL CTE planner
├── similarity/   # MinHash + LSH structural similarity
├── semantic/     # Multi-signal scoring (tokens, directory, AST)
└── cli/          # Interactive TUI installer + artifact export/import

🤝 Contributing

Contributions are welcome! The project uses standard Rust tooling:

bash

# Run tests
cargo test

# Lint
cargo clippy -- -D warnings

# Format
cargo fmt --all

📄 License

Apache-2.0