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development assistant bridging Obsidian vaults with Claude Code via MCP","maintainers":[{"name":"demgun","email":"youngbld102@gmail.com"}],"readme":"# Claude Brain\r\n\r\n[![Version](https://img.shields.io/badge/version-0.30.3-blue.svg)](package.json)\r\n[![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)\r\n[![Runtime](https://img.shields.io/badge/runtime-Bun-f472b6.svg)](https://bun.sh)\r\n\r\nA locally-running development assistant that bridges Obsidian knowledge vaults with Claude Code through the Model Context Protocol (MCP).\r\n\r\n## Features\r\n\r\n- Eliminates repetitive context explanations to Claude Code\r\n- Maintains project memory across sessions using Obsidian vault\r\n- Semantic memory system learns from past decisions (ChromaDB + SQLite)\r\n- **25 MCP tools** for context retrieval, memory storage, and intelligence\r\n- **Knowledge graph** connecting technologies, decisions, and concepts\r\n- **Episodic memory** with session detection and extractive summarization\r\n- **Hybrid retrieval** with BM25 + semantic fusion and cross-encoder reranking\r\n- **Temporal intelligence** for decision timelines, evolution tracking, and trend detection\r\n- **Multi-hop reasoning** with chain retrieval and what-if analysis\r\n- **Predictive intelligence** with context-aware recommendations\r\n- **Cross-project intelligence** for pattern discovery and knowledge transfer\r\n- **Semantic caching** with cosine similarity matching for fast repeated queries\r\n- **Event-driven orchestrator** for automatic file change handling\r\n- **Automatic duplicate prevention** for decisions (>90% similarity detection)\r\n- **Zod-validated tool inputs** for robust error handling\r\n- Runs completely locally with zero cloud dependencies\r\n- Compiles to single portable executable\r\n\r\n## Quick Start\r\n\r\n```bash\r\n# Install globally (requires Bun)\r\nbun install -g claude-brain\r\n\r\n# Interactive setup (vault path, log level, installs ~/.claude/CLAUDE.md)\r\nclaude-brain setup\r\n\r\n# Register with Claude Code\r\nclaude mcp add claude-brain -s user -- bunx claude-brain@latest\r\n```\r\n\r\nThat's it. Every Claude Code session now has 25 brain tools available.\r\n\r\n## Zero-Install Alternative\r\n\r\nSkip the global install — just register with Claude Code directly:\r\n\r\n```bash\r\nclaude mcp add claude-brain -s user -- bunx claude-brain@latest\r\n```\r\n\r\nOn first run, `~/.claude-brain/` is auto-created with default config.\r\n\r\n## Prerequisites\r\n\r\n- [Bun](https://bun.sh) >= 1.0.0\r\n- An Obsidian vault (or any markdown folder)\r\n\r\n## CLI Commands\r\n\r\n| Command | Description |\r\n|---------|-------------|\r\n| `claude-brain` | Start MCP server (default) |\r\n| `claude-brain setup` | Interactive setup wizard (run once per machine) |\r\n| `claude-brain install` | Register as MCP server in Claude Code |\r\n| `claude-brain uninstall` | Remove MCP server from Claude Code |\r\n| `claude-brain update` | Update package and refresh CLAUDE.md to latest |\r\n| `claude-brain health` | Run health checks |\r\n| `claude-brain diagnose` | Run diagnostics |\r\n| `claude-brain version` | Show version |\r\n| `claude-brain help` | Show help |\r\n\r\n## Documentation\r\n\r\nComprehensive documentation is available in the [`docs/`](docs/) directory:\r\n\r\n| Document | Description |\r\n|----------|-------------|\r\n| [API Reference](docs/API.md) | Complete HTTP API reference — 27 endpoints with request/response schemas and curl examples |\r\n| [Configuration](docs/CONFIGURATION.md) | Every config option documented with types, defaults, and environment variables |\r\n| [Knowledge Packs](docs/PACKS.md) | Pack format, built-in packs, custom pack creation, CLI commands |\r\n| [Hooks & Passive Learning](docs/HOOKS.md) | Hook system architecture, passive classification, git capture, session tracking |\r\n| [Code Intelligence](docs/CODE-INTELLIGENCE.md) | Tree-sitter indexing, `search_code` tool, supported languages, code-memory linking |\r\n| [Security Hardening](docs/SECURITY.md) | Authentication, TLS proxy configs, database security, incident response |\r\n| [Troubleshooting](docs/TROUBLESHOOTING.md) | 16 common issues with symptoms, causes, and solutions |\r\n| [Production Checklist](docs/PRODUCTION-CHECKLIST.md) | Pre/post deployment checklists, systemd/pm2 configs, backup & recovery |\r\n\r\n## Configuration\r\n\r\nConfiguration lives in `~/.claude-brain/.env`. Created automatically by `claude-brain setup`, or on first run with defaults. See [docs/CONFIGURATION.md](docs/CONFIGURATION.md) for the full reference (40+ options).\r\n\r\n| Variable | Description | Default |\r\n|----------|-------------|---------|\r\n| `VAULT_PATH` | Path to your Obsidian vault | `~/.claude-brain/vault` |\r\n| `LOG_LEVEL` | Log level (debug/info/warn/error) | `info` |\r\n| `NODE_ENV` | Environment | `production` |\r\n| `CLAUDE_BRAIN_HOME` | Override home directory | `~/.claude-brain/` |\r\n| `CLAUDE_BRAIN_API_KEY` | API key for HTTP endpoint auth | *(none)* |\r\n| `PORT` | HTTP API server port | `3333` |\r\n\r\n## Development\r\n\r\n```bash\r\n# Clone and install dependencies\r\ngit clone <repo-url>\r\ncd claude-brain\r\nbun install\r\n\r\n# Start dev server (uses local ./data, ./logs)\r\nbun run dev\r\n\r\n# Run tests\r\nbun test\r\n\r\n# Run tests in watch mode\r\nbun test --watch\r\n```\r\n\r\nThe `dev` script sets `CLAUDE_BRAIN_HOME=.` so all data stays in the project directory.\r\n\r\n## Building\r\n\r\n```bash\r\n# Build standalone executable for current platform\r\nbun run build:binary\r\n\r\n# Build for all platforms (Windows, macOS, Linux)\r\nbun run build:all\r\n```\r\n\r\n## Project Structure\r\n\r\n```\r\nclaude-brain/\r\n├── src/\r\n│   ├── index.ts              # Entry point (thin wrapper)\r\n│   ├── cli/\r\n│   │   ├── bin.ts            # CLI entry point (claude-brain command)\r\n│   │   ├── auto-setup.ts     # First-run home directory initialization\r\n│   │   └── commands/         # serve, install-mcp, uninstall-mcp, update\r\n│   ├── config/\r\n│   │   ├── home.ts           # ~/.claude-brain/ path resolution\r\n│   │   ├── loader.ts         # Config loading (defaults → file → env)\r\n│   │   └── schema.ts         # Zod config schemas\r\n│   ├── server/               # MCP server code\r\n│   │   └── handlers/tools/   # 25 tool handlers with Zod validation\r\n│   ├── vault/                # Obsidian integration\r\n│   ├── memory/               # Vector DB & embeddings\r\n│   │   ├── chroma/           # ChromaDB integration with duplicate detection\r\n│   │   ├── episodic/         # Session detection & episode management\r\n│   │   └── consolidation/    # Memory importance scoring & archival\r\n│   ├── knowledge/            # Knowledge graph & entity extraction\r\n│   │   └── graph/            # In-memory graph with search & auto-population\r\n│   ├── retrieval/            # Hybrid search (BM25 + semantic + reranking)\r\n│   ├── temporal/             # Timeline construction & trend detection\r\n│   ├── reasoning/            # Multi-hop chain retrieval & what-if analysis\r\n│   ├── prediction/           # Decision prediction & recommendations\r\n│   ├── cross-project/        # Cross-project pattern discovery & transfer\r\n│   ├── optimization/         # Semantic caching & precomputation\r\n│   ├── orchestrator/         # Event-driven coordination system\r\n│   ├── setup/                # Interactive setup wizard\r\n│   ├── context/              # Context assembly\r\n│   ├── tools/                # MCP tool definitions & registry\r\n│   └── utils/                # Shared utilities\r\n├── assets/\r\n│   └── CLAUDE.md             # Protocol file (shipped with npm package)\r\n├── tests/                    # 750+ tests\r\n└── ~/.claude-brain/          # User data (created at runtime)\r\n    ├── .env                  # Configuration\r\n    ├── data/                 # SQLite + ChromaDB\r\n    ├── logs/                 # Log files\r\n    └── vault/                # Default vault location\r\n```\r\n\r\n## Architecture Highlights\r\n\r\n### Event-Driven Orchestrator\r\nThe orchestrator automatically responds to file changes in your vault:\r\n- Detects new decisions in `decisions.md` files\r\n- Triggers automatic semantic indexing\r\n- Coordinates between vault, memory, and context systems\r\n\r\n### Duplicate Prevention\r\nWhen storing decisions, the system:\r\n- Searches for existing decisions with >90% semantic similarity\r\n- Returns existing ID if duplicate found (prevents bloat)\r\n- Logs skipped duplicates for transparency\r\n\r\n### Input Validation\r\nAll tool inputs are validated using Zod schemas:\r\n- Clear error messages for invalid parameters\r\n- Type-safe extraction of validated inputs\r\n- Consistent validation across all 25 tools\r\n\r\n### Embedding Cache\r\nUses SHA-256 hashing for cache keys to prevent collisions (improved from simple hash).\r\n\r\n### MCP Tools (25 total)\r\n\r\n| Category | Tools |\r\n|----------|-------|\r\n| Context Retrieval | `get_project_context`, `smart_context`, `recall_similar`, `get_code_standards`, `get_phase12_status` |\r\n| Memory Storage | `remember_decision`, `auto_remember`, `recognize_pattern`, `record_correction`, `update_progress` |\r\n| Project Management | `list_projects`, `create_project`, `init_project` |\r\n| Knowledge Graph | `search_knowledge_graph`, `get_episode`, `list_episodes` |\r\n| Patterns & Corrections | `get_patterns`, `get_corrections` |\r\n| Feedback | `rate_memory` |\r\n| Advanced Intelligence | `get_decision_timeline`, `analyze_decision_evolution`, `detect_trends`, `what_if_analysis`, `get_recommendations`, `find_cross_project_patterns` |\r\n\r\n## Security\r\n\r\nFor production deployments, see [docs/SECURITY.md](docs/SECURITY.md). Key recommendations:\r\n\r\n- **Always set `CLAUDE_BRAIN_API_KEY`** in production — generate with `openssl rand -hex 32`\r\n- Server binds to **localhost only** by default — use a reverse proxy for remote access\r\n- CORS is restricted to localhost — add explicit origins via `corsOrigins` config\r\n- Rate limiting is enabled by default (200 req/60s)\r\n- All file operations are protected against path traversal\r\n\r\n## API\r\n\r\nClaude Brain exposes an HTTP API on port 3333 (default) for programmatic access. See [docs/API.md](docs/API.md) for the full reference.\r\n\r\n```bash\r\n# Health check\r\ncurl http://localhost:3333/api/health\r\n\r\n# Store a memory (requires API key)\r\ncurl -X POST http://localhost:3333/api/memory \\\r\n  -H \"Content-Type: application/json\" \\\r\n  -H \"X-API-Key: your-key\" \\\r\n  -d '{\"content\": \"Use ESM imports\", \"project\": \"my-app\", \"category\": \"decision\"}'\r\n\r\n# Search memories\r\ncurl \"http://localhost:3333/api/search?q=imports&project=my-app\" \\\r\n  -H \"X-API-Key: your-key\"\r\n```\r\n\r\n## License\r\n\r\nMIT\r\n","readmeFilename":"README.md"}