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Directory Structure

src
├── main.ts             # Runtime entrypoint that starts the CLI or MCP server.
├── assets/             # Packaged grammar registry, ignore-rule assets, prompt templates, and other static runtime assets.
├── database/           # SQLite schema, low-level actions, service adapters, migrations, and database policy helpers.
│   ├── actions/        # Focused database reads/writes and transaction/bootstrap helpers.
│   ├── services/       # Persistence-backed implementations for memory, project, status, transfer, and taxonomy workflows.
│   ├── support/        # Database-specific policies, scoring, transfer types, and retrieval text helpers.
│   └── utils/          # Database utilities, including raw SQL migrations.
├── entrypoints/        # Protocol adapters for external callers.
│   ├── cli/            # Commander command classes, subcommands, registry, and shared BaseCommand.
│   └── mcp/            # MCP tools, prompts, schemas, error handling, and tool output helpers.
├── modules/            # Application workflows and concrete runtime capabilities.
│   ├── cli/            # CLI workflow helpers such as grammar selection.
│   ├── embeddings/     # Embedding providers and embedding generation pipeline.
│   ├── extraction/     # Project extraction orchestration and extraction engine internals.
│   ├── memory/         # Recall, save, transfer, and runtime wiring for memory workflows.
│   └── project/        # Project context, source classification, and warm-up ranking.
├── support/            # Project-owned generic utilities and test-light infrastructure helpers.
│   ├── cli/            # CLI user error and JSON output helpers.
│   ├── format/         # Number and token formatting/estimation helpers.
│   ├── json/           # JSON file I/O helpers.
│   ├── object/         # Generic object/value helpers.
│   ├── terminal/       # Terminal output and color helpers.
│   └── tui/            # Small terminal UI components.
└── types/              # Shared domain contracts and public data shapes.

tests
├── fake/               # Test doubles shared across feature and unit tests.
├── features/           # Comprehensive behavior, integration, CLI, MCP, storage, and workflow tests.
├── support/            # Test support utilities.
└── units/              # Focused unit tests for small policies, mappers, schemas, and helpers.

Code Flow

Entrypoints translate CLI and MCP protocol concerns into application requests. Modules own workflow orchestration and runtime capabilities. Database owns the SQLite boundary and persistence-backed service implementations. Shared domain types stay in types, and generic helpers stay in support.

graph LR
    E[main.ts] --> C[entrypoints/cli]
    E --> Q[entrypoints/mcp]
    C --> M[modules]
    Q --> M
    M --> D[database/services]
    D --> A[database/actions]
    A --> S[database/schema and migrations]
    M --> O[modules/persistence]
    C --> T[types]
    Q --> T
    M --> T
    D --> T
    C --> U[support]
    Q --> U
    M --> U
    D --> U
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