- Annotate 43 tool domain classes (contract/projection/boundary/store/adapter/mysql) - Add tool registration and execution chain learning note - Add tool call chain runtime journey note (model decision to observation)
- Annotate DiagnosisProgressTracker, HarnessToolInterceptor, DiagnosisProgressProjector, DiagnosisReleaseUseCase, ToolBoundary, ToolBoundaryResult, CanonicalToolInvocation - Add progress code learning note: interceptor gates, tracker state machine, canonical lifecycle, execution gate, projection/release pipeline - Update learning roadmap: progress marked as deeply learned, next is tool domain
Relocate RAG and diagnosis decision/E2E writeups from docs/ root into mvp/engineering so architecture, issues, and engineering narrative stay together. Update indexes and cross-links; leave docs/learning as legacy.