feat: enhance agent reasoning observability and remove turn duration clutter

feat(agents): full implementation of harness engineering and file sync fixes ...

- Implemented Area 1: Backend scaffolding, CRUD, schemas, and session locking
- Implemented Area 2: Agent execution loop, RAG integration, and Circuit Breaker
- Updated UI: Configure CRON triggers, Target Mesh nodes, and display system prompt in Agent Drilldown
- Fixed LLM fallback resolving vertex_ai_beta
- Fixed File System Sync pseudo-nodes (hub, local) raising 'Offline'
- Fixed FileSystemNavigator initialPath bug causing synced files not to render in UI Mesh Workspace

docs: Auto-generate latest API reference documentation