Constructor with nullable dependencies.
For Phase 1 (config registration): project_manager can be null. For Phase 2 (tool instance creation): project_manager is provided.
If project_manager is provided, init_dependencies() is called automatically. Vector database is not created in constructor (requires async operation). Call init_databases() after construction to create the vector database.
| project_manager |
Project manager for accessing active project and database (nullable for Phase 1) |