* Update project creation and retrieval to use generated models
* Modify skill addition and listing to utilize generated models
* Refactor thought handling to incorporate generated models
* Adjust tool annotations to align with new model structure
* Update API calls in the UI to use new ResolveSpec-based endpoints
* Enhance stats retrieval logic to aggregate thought metadata
* Implement DescribeTool for listing available MCP tools with annotations.
* Add UpsertToolAnnotation and GetToolAnnotations methods for managing tool notes.
* Create tool_annotations table for storing tool usage notes.