sigil-mcp-server 1.0.0

Model Context Protocol server for IDE-like code navigation and semantic search

Sigil MCP Server

A Model Context Protocol (MCP) server that provides IDE-like code navigation and search for local repositories. Gives AI assistants like ChatGPT powerful code exploration capabilities including symbol search, trigram indexing, and semantic navigation.

Features

Hybrid Code Search

• Fast text search using trigram indexing (inspired by GitHub's Blackbird)
• Trigram store uses RocksDB via rocksdict (install with pip install -e .[trigrams-rocksdict]); SQLite fallback is removed.
• Symbol-based search for functions, classes, methods, and variables
• Semantic code search with vector embeddings backed by LanceDB (ANN queries, per-repo vector stores)
• File structure view showing code outlines
• Automatic index updates with file watching (optional)

Production Ready

• Thread-safe concurrent access (SQLite WAL mode + RLock serialization)
• File watcher, HTTP handlers, and vector indexing run safely in parallel
• No "database is locked" errors from concurrent operations
• Admin API for operational management (index rebuilds, stats, logs)
• Comprehensive request/response logging with header redaction

Enterprise Security

• OAuth 2.0 authentication with PKCE support for remote access
• Local connection bypass (no auth needed for localhost)
• API key fallback and IP whitelisting

Available Tools

• index_repository - Build searchable index with symbol extraction
• search_code - Fast substring search across repositories
• goto_definition - Find symbol definitions
• list_symbols - View file/repo structure
• list_mcp_tools, external_mcp_prompt - Discover external MCP tools registered into Sigil
• build_vector_index - Generate semantic embeddings for code (optional)
• semantic_search - Natural language code search using embeddings
• list_repos, read_repo_file, list_repo_files, search_repo - Basic operations
• get_index_stats, ping - Server info and health checks

Quick Start

Installation

Clone and install dependencies:

git clone https://github.com/Superuser666-Sigil/SigilDERG-Custom-MCP.git
cd SigilDERG-Custom-MCP
pip install -e .[server-full]

Default embedding runtime: llamacpp with Jina v2 code embeddings (768-dim) at ./models/jina/jina-embeddings-v2-base-code-Q4_K_M.gguf.

Install Universal Ctags for symbol extraction (optional but recommended):

macOS: brew install universal-ctags Ubuntu/Debian: sudo apt install universal-ctags Arch Linux: sudo pacman -S ctags

Configuration

Copy the example config and edit with your repository paths:

cp config.example.json config.json
# Edit config.json

Example configuration:

{
  "repositories": {
    "my_project": "/absolute/path/to/your/project",
    "another_repo": "/path/to/another/repo"
  }
}

Alternatively, use environment variables:

export SIGIL_REPO_MAP="my_project:/path/to/project;another:/path/to/another"

Running the Server

Recommended: Use the restart script (starts both MCP server and Admin UI):

./scripts/restart_servers.sh

This script will:

• Stop any running server processes
• Start the MCP Server on port 8000
• Start the Admin UI frontend on port 5173
• Run both processes with nohup so they persist after terminal closes

Manual start (MCP server only):

python -m sigil_mcp.server

Stop all servers:

./scripts/restart_servers.sh --stop

On first run, OAuth credentials will be generated. Save the Client ID and Client Secret for connecting from ChatGPT.

Connecting to ChatGPT

[!IMPORTANT] Using Cloudflare Tunnel? You must disable Bot Fight Mode or ChatGPT's OAuth will fail.
📖 See Cloudflare OAuth Issue & Solution for details.

1. Expose via ngrok: ngrok http 8000 (or use Cloudflare Tunnel)
2. In ChatGPT, add MCP connector with OAuth authentication
3. Use the OAuth credentials from server startup
4. Start using: "Search my code for async functions"

Important: The server is configured for ChatGPT compatibility:

• DNS rebinding protection is disabled (ChatGPT sends ngrok Host headers)
• MCP endpoint mounted at root / (not /mcp)
• OAuth authentication remains active and required

See docs/CHATGPT_SETUP.md for detailed instructions.

Usage Examples

Once connected to ChatGPT as an MCP server:

You: "Index my project repository"
ChatGPT: Indexed 342 files, found 1,847 symbols in 3.2 seconds

You: "Find where the HttpClient class is defined"
ChatGPT: Found in project::src/http/client.py at line 45

You: "Search for async functions"
ChatGPT: Found 23 matches across 8 files

You: "Build vector index for semantic search"
ChatGPT: Indexed 856 chunks from 342 documents

You: "Find code that handles user authentication"
ChatGPT: Found 5 relevant code sections (semantic search):
  - auth/handlers.py:45-145 (score: 0.89)
  - middleware/auth.py:12-112 (score: 0.84)
  ...

Architecture

Indexing Process

1. File scanning (skips build artifacts)
2. Content storage with SHA-256 deduplication
3. Symbol extraction via universal-ctags
4. Trigram inverted index generation
5. Compression using zlib

Storage

~/.sigil_index/
├── repos.db           # SQLite: repos, documents, symbols
├── trigrams.rocksdb/  # RocksDB trigram inverted index (default, via rocksdict)
├── lancedb/       # LanceDB vector store (per-repo code_vectors tables + PQ indexes)
└── blobs/         # Compressed content

Performance

• Symbol lookup: O(log n) via SQLite indexes
• Text search: O(k) where k = trigrams * documents per trigram
• Typical query latency: 10-100ms

Security

Path Traversal Protection: All paths validated to prevent escaping repository roots

Authentication Layers: OAuth 2.0 (primary), Local bypass (localhost), API keys (fallback), IP whitelist (optional)

Protection: Source code requires authentication for remote access, OAuth credentials stored with 0600 permissions, tokens expire after 1 hour with refresh support, PKCE prevents authorization code interception

ChatGPT Compatibility: For ChatGPT MCP connector compatibility, DNS rebinding protection is disabled. This means:

• [NO] Host header validation: Disabled (accepts ngrok domains)
• [NO] Content-Type validation: Disabled (accepts application/octet-stream)
• [YES] OAuth 2.0 authentication: Active and required
• [YES] Bearer token validation: Active
• [YES] Token expiration: Enforced

See docs/SECURITY.md for detailed security documentation.

Documentation

Setup Guides

• ChatGPT Setup Guide
• OAuth Configuration
• Cloudflare Tunnel Deployment
• Security Best Practices
• Operations Runbook
• Troubleshooting Guide
• Llama.cpp Local Embeddings
• Vector Embeddings Usage Guide
• Embedding Setup Guide

Architecture Decision Records (ADRs)

• ADR-001: OAuth 2.0 Authentication
• ADR-002: Trigram-Based Indexing (superseded)
• ADR-003: Symbol Extraction with Ctags
• ADR-004: JSON Configuration System
• ADR-005: FastMCP Custom Routes
• ADR-006: Vector Embeddings for Semantic Search
• ADR-007: File Watching
• ADR-008: Granular Re-indexing and Configurable Patterns
• ADR-009: ChatGPT MCP Connector Compatibility
• ADR-010: Thread Safety and SQLite WAL Mode
• ADR-011: Admin API for Operational Management
• ADR-012: ASGI Header Logging Middleware
• ADR-013: LanceDB Vector Store Migration
• ADR-014: Admin UI Testing Strategy
• ADR-015: Default Llama.cpp + Jina Embeddings
• ADR-016: External MCP Aggregation
• ADR-017: RocksDB Trigram Store

Other

• ChatGPT OAuth Configuration
• Cloudflare 502 Fix
• Cloudflare OAuth Issue
• External MCP Integration (if exists, otherwise see config.example.json)

Contributing

Contributions welcome! Please see CONTRIBUTING.md for guidelines including:

• Contributor License Agreement (CLA) - Required for all contributors
• Developer Certificate of Origin (DCO) requirements
• Code standards and testing requirements
• Pull request process
• Code of Conduct

Licensing

Sigil is dual-licensed:

• Open Source: Available under AGPLv3 for open-source projects and private use where source sharing requirements are met.

• Commercial: A commercial license is required for organizations who wish to run Sigil internally without open-sourcing their own applications or who need indemnification and support.

Contact me for commercial licensing options.

See LICENSE file for full AGPLv3 text.

Licensing FAQ

Q: Can I run this inside my company under AGPLv3?

A: Yes, as long as you're comfortable with AGPLv3 and its requirements. If you expose the server to users over a network (like running it as an internal service), AGPLv3 requires making the source code available to those users, including any modifications you've made.

Q: We have a "no AGPL" policy. Can we still use Sigil?

A: Yes, via a commercial license. Email [e-mail] to discuss your needs.

Q: Why do I have to sign a CLA to contribute?

A: The Contributor License Agreement keeps the licensing story clean—AGPLv3 for the open-source community, commercial licenses for organizations that need them—without legal ambiguity about who owns what. Your contribution remains open-source under AGPLv3; the CLA just clarifies the rights.

Q: What's included in a commercial license?

A: Commercial licenses provide freedom to use Sigil internally without open-source requirements, ability to keep modifications proprietary, indemnification and support options, and clear legal status for enterprise compliance. Contact me for details and pricing.

Q: Can I use this for my personal projects?

A: Absolutely! AGPLv3 is perfect for personal projects, hobbyist use, and small teams. You only need a commercial license if you have organizational requirements that conflict with AGPL.

For more details on contributing, see CONTRIBUTING.md.

Acknowledgments

• Trigram indexing inspired by GitHub's Blackbird search engine
• Symbol extraction powered by Universal Ctags
• Built on the Model Context Protocol (MCP) specification

Support

Issues: GitHub Issues Documentation: docs/ Security: docs/SECURITY.md