Codebase Synapse

Indexes codebase into a local knowledge graph with 40+ AI tools and codebase-guard.

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

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

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Documentation Overview

🧠 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

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about Codebase Synapse

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "codebase-synapse": { "command": "npx", "args": ["-y", "codebase-synapse"] } }

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Technical Specs & Signals

CategoryDeveloper Tools

37Quality signal: Fair · 37/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools16/30

Adoption & activity2/15

Community engagement0/10

A guidance signal from public completeness & health data — not a user rating. New listings start lower and rise as they add docs, get verified, and grow adoption. Signals we can't observe for a listing are skipped, not counted against it.

★ Featured

Moxie Docs MCP

MCP & Agent Skills for Automated Documentation, and codebase conventions + context

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More in 💻 Developer Tools →Best MCP servers for Developers →Alternatives to Codebase Synapse →Install in Claude Desktop Install in Cursor Install in VS Code

Codebase Synapse

Indexes codebase into a local knowledge graph with 40+ AI tools and codebase-guard.

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

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

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Documentation Overview

🧠 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

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

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

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

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about Codebase Synapse

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "codebase-synapse": { "command": "npx", "args": ["-y", "codebase-synapse"] } }

AllMCPs Directory Badge

Full Badge Customizer

Showcase your server listing on GitHub or your project documentation. Embed this dynamic SVG badge to highlight official listing status and live engagement.

Badge Style:

Live Dynamic SVG Preview

Markdown (GitHub README)

[![AllMCPs](https://allmcps.com/api/badge/codebase-synapse?style=directory)](https://allmcps.com/mcp/codebase-synapse)

HTML Embed

<a href="https://allmcps.com/mcp/codebase-synapse"><img src="https://allmcps.com/api/badge/codebase-synapse?style=directory" alt="Codebase Synapse on AllMCPs" /></a>

Technical Specs & Signals

CategoryDeveloper Tools

37Quality signal: Fair · 37/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools16/30

Adoption & activity2/15

Community engagement0/10

★ Featured

Moxie Docs MCP

MCP & Agent Skills for Automated Documentation, and codebase conventions + context

Explore Server →

Own this project?

Free dofollow backlink: add your website and place the AllMCPs badge on it — no claim needed. We detect it automatically and keep it verified as long as the badge stays live.

Claim & get free dofollow

Share & Embed

Add our SVG badge (dark/light directory styles) or embeddable widget to your site.

Explore more

More in 💻 Developer Tools →Best MCP servers for Developers →Alternatives to Codebase Synapse →Install in Claude Desktop Install in Cursor Install in VS Code