# Docker running (for PostgreSQL + pgvector)
docker ps | grep codebrain

# Node.js 20+
node --version

# Dependencies installed
cd /Users/conorandrle/Documents/Coding/CodeBrainMCP/CodeBrain
pnpm install

# Start PostgreSQL with pgvector (if not running)
docker run -d \
  --name codebrain \
  -p 5484:5432 \
  -e POSTGRES_PASSWORD=postgres \
  -e POSTGRES_DB=codebrain \
  pgvector/pgvector:pg15

# Setup database schema
pnpm db:setup
pnpm db:migrate

GEMINI_API_KEY=your_api_key_here
DATABASE_URL=postgresql://postgres:postgres@localhost:5484/codebrain?schema=cbmcp

# Run tests
pnpm test

# Should show: ✅ 28 tests passed

# Test MCP server starts
npx tsx src/index.ts
# Should output: 🚀 CodeBrain MCP Server started (stdio mode)
# Press Ctrl+C to stop

{
  "command": "npx",
  "args": [
    "-y",
    "tsx",
    "/Users/conorandrle/Documents/Coding/CodeBrainMCP/CodeBrain/src/index.ts"
  ],
  "env": {
    "GEMINI_API_KEY": "your_key_here",
    "DATABASE_URL": "postgresql://postgres:postgres@localhost:5484/codebrain?schema=cbmcp"
  }
}

{
  "mcpServers": {
    "codebrain": {
      "command": "npx",
      "args": [
        "-y",
        "tsx",
        "/Users/conorandrle/Documents/Coding/CodeBrainMCP/CodeBrain/src/index.ts"
      ],
      "env": {
        "GEMINI_API_KEY": "your_key_here",
        "DATABASE_URL": "postgresql://postgres:postgres@localhost:5484/codebrain?schema=cbmcp"
      }
    }
  }
}

{
  projectName: string;   // Unique project identifier
  rootPath: string;      // Absolute path to code
  force?: boolean;       // Re-index existing files
}

{
  query: string;         // What to search for
  projectName?: string;  // Filter by project
  topK?: number;        // Number of results (default: 5)
  threshold?: number;   // Similarity threshold (default: 0.5)
}

{
  projectName: string;   // Project to query
}

┌─────────────────────────────────────────────┐
│         Cursor / Claude Desktop             │
│              (MCP Client)                   │
└─────────────────┬───────────────────────────┘
                  │ MCP Protocol (stdio)
                  │
┌─────────────────▼───────────────────────────┐
│         CodeBrain MCP Server                │
│  ┌─────────────────────────────────────┐   │
│  │  AST Code Splitter                  │   │
│  │  - JavaScript/TypeScript            │   │
│  │  - Python, Go, Rust, Java, C++      │   │
│  └──────────────┬──────────────────────┘   │
│                 │                           │
│  ┌──────────────▼──────────────────────┐   │
│  │  Gemini Embeddings                  │   │
│  │  - 768-dimensional vectors          │   │
│  │  - Semantic descriptions            │   │
│  └──────────────┬──────────────────────┘   │
│                 │                           │
│  ┌──────────────▼──────────────────────┐   │
│  │  Vector Search                      │   │
│  │  - Cosine similarity                │   │
│  │  - Threshold filtering              │   │
│  └──────────────┬──────────────────────┘   │
└─────────────────┼───────────────────────────┘
                  │
┌─────────────────▼───────────────────────────┐
│      PostgreSQL + pgvector                  │
│  ┌──────────────────────────────────────┐  │
│  │  Projects → Files → Chunks → Embeds │  │
│  │  Normalized relational schema        │  │
│  └──────────────────────────────────────┘  │
└─────────────────────────────────────────────┘

# Run all tests
pnpm test

# Watch mode
pnpm test:watch

# Individual test suites
pnpm test:splitter     # AST code splitter
pnpm test:indexing     # Indexing workflow
pnpm test:search       # Semantic search
pnpm test:embedding    # Embedding generation

# Integration test (end-to-end)
pnpm test:integration

# Start the Graph API server (serves graph JSON on http://localhost:4000)
pnpm graph:server

# In a separate terminal, install and run the viewer UI
cd apps/graph-viewer
pnpm install
pnpm dev

# Open the browser UI → http://localhost:5173

CodeBrain/
├── src/
│   ├── index.ts              # MCP server entry point
│   ├── core/
│   │   ├── indexing.ts       # Indexing orchestration
│   │   ├── search.ts         # Semantic search
│   │   ├── splitter.ts       # AST-based code splitting
│   │   └── embedding/
│   │       ├── base-embedding.ts      # Embedding interface
│   │       └── gemini-embedding.ts    # Gemini implementation
│   └── test/
│       ├── *.test.ts         # Unit tests
│       └── utils.ts          # Test utilities
├── db/
│   ├── index.ts              # Prisma client
│   ├── setup.ts              # Database setup script
│   └── vector-indexes.ts     # Vector index management
├── prisma/
│   └── schema.prisma         # Database schema
├── .env                      # Environment variables
├── mcp-config.json          # MCP configuration template
├── CURSOR_SETUP.md          # Cursor integration guide
└── README.md                # This file

Project (1) ─┐
             ├─> File (N) ─┐
                           ├─> Chunk (N) ─┐
                                          ├─> Embedding (N)

pnpm dev              # Start with auto-reload
pnpm start            # Start server
pnpm build            # Compile TypeScript

pnpm db:setup         # Setup database + pgvector
pnpm db:migrate       # Run migrations
pnpm db:generate      # Generate Prisma client
pnpm db:studio        # Open Prisma Studio

# Required
GEMINI_API_KEY=your_gemini_api_key
DATABASE_URL=postgresql://user:pass@host:port/db?schema=cbmcp

# Optional
NODE_ENV=development

pnpm db:setup  # This installs pgvector in cbmcp schema

docker ps | grep codebrain  # Verify container running
docker start codebrain      # Start if stopped