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Your source code never leaves your machine.\n\n[![CI](https://github.com/giauphan/codeatlas-mcp-server/actions/workflows/ci.yml/badge.svg)](https://github.com/giauphan/codeatlas-mcp-server/actions/workflows/ci.yml)\n[![Node.js Version](https://img.shields.io/badge/node-%3E%3D20.0.0-brightgreen)](https://nodejs.org/)\n[![License: MIT](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n[![GitHub Release](https://img.shields.io/github/v/release/giauphan/codeatlas-mcp-server)](https://github.com/giauphan/codeatlas-mcp-server/releases)\n\n## 📌 What is CodeAtlas MCP Server?\n\nA **Model Context Protocol (MCP)** server that provides:\n- **AST Analysis**: Parse TypeScript, Python, PHP, and more.\n- **Dependency Graphs**: Visualize call chains and module relationships.\n- **Semantic Search**: Find code by meaning, not just syntax.\n- **Local-First**: Your code stays on your machine; no telemetry by default.\n- **Cloud Optional**: Connect to [codeatlas-platform](https://github.com/giauphan/codeatlas-platform) for dream memory, genome immune system, and skills sync.\n\n### Why Use It?\n| Use Case | Benefit |\n|---|---|\n| **AI IDE Integration** | Claude Desktop, Cursor, VSCode — get context-aware code intelligence. |\n| **Codebase Audits** | Automate dependency analysis, security scans, and refactoring insights. |\n| **Semantic Search** | Find functions, classes, or modules by intent, not just name. |\n| **Multi-Language Support** | Works with TypeScript, Python, PHP, and more via AST parsers. |\n\n---\n\n## 🏗 Architecture\n\n```\nAI IDE → MCP stdio/SSE → Parser (AST) → Dependency Graph → Code Search\n                          │\n                    codeatlas-platform (HTTP) → Dreams + Genome\n```\n\n| Layer | Components |\n|---|---|\n| **Parser** | TypeScript, Python, PHP AST analysis |\n| **Graph** | Dependency graph with chunked force layout |\n| **Search** | Semantic code search with regex safety |\n| **Cloud** | Optional: connect to codeatlas-platform for dreams/genome |\n\n---\n\n## 🔧 Quick Start\n\n### 1. Install\n```bash\n# Clone the repo\ngit clone https://github.com/giauphan/codeatlas-mcp-server.git\ncd codeatlas-mcp-server\n\n# Install dependencies (requires Node.js 20+)\npnpm install\n```\n\n### 2. Configure\n```bash\n# Copy env template\ncp .env.example .env\n\n# Edit .env (Oracle DB optional for persistent memory)\n# Cloud features require both variables; no default URL is used\n# Set CODEATLAS_API_URL to your CodeAtlas API base URL\n# Set CODEATLAS_API_KEY to your CodeAtlas API key\n```\n\n### 3. Build\n```bash\npnpm run build\n```\n\n### 4. Run\n```bash\n# Local-only mode (no cloud)\npnpm start\n\n# With cloud connection (requires codeatlas-platform running)\nCODEATLAS_API_URL=http://localhost:8080 CODEATLAS_API_KEY=your_api_key_here pnpm start\n```\n\n---\n\n## 📡 MCP Tools (30+)\n\n| Category | Tools |\n|---|---|\n| **Code Analysis** | `analyze_project`, `code_search`, `file_info` |\n| **AST** | `parse_file`, `find_symbol`, `get_dependencies` |\n| **Graphs** | `dependency_graph`, `call_graph` |\n| **Security** | `scan_vulnerabilities` |\n| **Cloud** | `save_dream_memory`, `query_dream_memories`, `sync_dreams` |\n| **Skills** | `search_skills`, `get_skill`, `install_skill` |\n\n### Example: Connect to Claude Desktop\nAdd to `claude-desktop-config.json`:\n```json\n{\n  \"mcpServers\": {\n    \"codeatlas\": {\n      \"command\": \"npx\",\n      \"args\": [\n        \"-y\",\n        \"codeatlas-mcp-server\"\n      ]\n    }\n  }\n}\n```\n\n### Example: Connect to Cursor/VSCode (SSE)\nAdd to `settings.json`:\n```json\n{\n  \"mcp.sse\": {\n    \"codeatlas\": \"npx codeatlas-mcp-server\"\n  }\n}\n```\n\n### Connect to Zed (MCP context server)\nZed has no Claude-style hooks, so the Second Brain hooks are exposed as MCP tools instead.\n\n**Option A — automatic setup:**\n```bash\ncodeatlas-enterprise setup zed\n```\nThis writes a `codeatlas` entry into Zed's `context_servers` (passing `CODEATLAS_API_KEY`/`CODEATLAS_API_URL` from your environment). Restart Zed afterward.\n\n**Option B — manual:** add to Zed `settings.json` (open via `zed: open settings file`):\n```json\n{\n  \"context_servers\": {\n    \"codeatlas\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"codeatlas-mcp-server\"],\n      \"env\": { \"CODEATLAS_API_KEY\": \"your_api_key_here\" }\n    }\n  }\n}\n```\n\nThen in Zed's Agent Panel, call the `brain_context` tool at the start of a task to inject Second Brain memory, and `save_dream_memory` after a task to persist learnings. `route_task` suggests a model/effort (advisory only — Zed does not auto-switch models). See [Zed Integration](./docs/ZED_INTEGRATION.md).\n\n---\n\n\n## 🔒 Security & Environment Variables\n\nCodeAtlas MCP Server is designed with a local-first architecture and several security hardening measures to protect your credentials and codebase data:\n\n- **No Disk Persistence**: Credentials like `CODEATLAS_API_KEY` are kept entirely in-memory and are **never** persisted to `.env` files or disk. You must supply your key via environment variables.\n- **Strict Destination Validation**: When connecting to cloud features, the destination AI and backend URLs are strictly validated. Credentials can only flow to trusted official domains (`*.codeatlas.ai`, `opencode.ai`) or local addresses (`localhost`, `127.0.0.1`).\n- **Telemetry & Logging**: Potential credential leaks are sanitized and redacted from all console and error logs.\n\n### Required & Optional Environment Variables\n\n| Variable | Description | Default |\n|---|---|---|\n| `CODEATLAS_API_KEY` | Secret key to connect to CodeAtlas Cloud services for AI memory and scan features. | (none) |\n| `CODEATLAS_API_URL` | Target URL for CodeAtlas Cloud. Validated via allowlists to prevent credential exfiltration. | `https://api.codeatlas.ai` |\n| `CODEATLAS_ALLOW_CUSTOM_URL` | Set to `true` to allow sending credentials to self-hosted or unlisted destinations. Required for private network deployments. | `false` |\n| `CODEATLAS_SCAN_AI_KEY` | Key for deep AI security scanning using an external LLM. | (none) |\n| `CODEATLAS_SCAN_AI_URL` | Endpoint for deep AI security scanning. | (none) |\n\n## 📚 Documentation\n\n| Guide | Description |\n|---|---|\n| [Development Guide](./docs/DEVELOPMENT.md) | Full environment setup, commands, and troubleshooting. |\n| [Deployment Guide](./docs/DEPLOYMENT.md) | PM2, systemd, Nginx TLS, and healthchecks. |\n| [API Examples](./docs/API_EXAMPLES.md) | Auth, dream memory, and MCP config examples. |\n\n---\n\n## 🤝 Contributing\n\nSee [CONTRIBUTING.md](./CONTRIBUTING.md) for guidelines.\n\n---\n\n## 📜 License\n\nMIT © [Giau Phan](mailto:giauphan012@gmail.com)\n\n---\n\n## 🔗 Related Projects\n\n- [codeatlas-platform](https://github.com/giauphan/codeatlas-platform) — HTTP server for dream memory and genome.\n- [codeatlas-mcp](https://www.npmjs.com/package/codeatlas-mcp) — npm package for easy installation.\n\n---\n\n## ⚠️ Known Limitations\n\n- **Oracle DB Required for Persistent Memory**: Local-only mode works without Oracle, but dream memory persistence requires it.\n- **Cloud Dream Query Filters**: When querying memories with `scope`, `tags`, or `memory_type` filters, the backend performs vector hybrid search on the query text plus SQL filtering on the other parameters. The `tags` parameter is passed as a JSON string to the upstream API. The `related_ids` parameter is also supported for filtering by related memory IDs.\n- **Multi-Tenant Not Supported**: Only single-tenant mode available.\n- **Security**: No built-in rate limiting; use a reverse proxy (Nginx) in production.\n\n---\n\n## 🐛 Issues & Support\n\n- Report bugs or request features: [GitHub Issues](https://github.com/giauphan/codeatlas-mcp-server/issues)\n- For questions: [Discussions](https://github.com/giauphan/codeatlas-mcp-server/discussions)\n","readmeFilename":"README.md"}