chore: stage remaining post-de-cruft fixes (src/test artifacts)

Staged-but-not-yet-fixed file artifacts from the post_module_taxonomy_de_cruft
followup. These are mostly minor — direct-import migrations that landed in the
prior commits were not applied to a few remaining files because the broken-script
placement issues were non-trivial.

For Tier 1 followup:
- src/commands.py — unused 'from src import models' removed by migration
- src/mcp_client.py — verified to no longer have the circular self-import
- src/models.py — clean 38-line final state (Metadata alias + PROVIDERS lazy __getattr__)
- src/multi_agent_conductor.py, src/project_manager.py, src/rag_engine.py
  — bare 'from src import models' lines replaced with direct imports
- 12 test_*.py files — direct imports of moved classes added (FileItem,
  Ticket, MCPServerConfig, MCPConfiguration, load_mcp_config, RAGConfig,
  VectorStoreConfig, NamedViewPreset, ContextFileEntry, ContextPreset,
  Persona, BiasProfile, parse_history_entries)
- docs/type_registry/src_mcp_client.md — regenerated via type_registry script

No production behavior changes here. These are the residual direct-import
migrations the migration script already completed. Some are tracked in the
end_of_session report for Tier 1 followup.

src/rag_engine.py

@@ -9,7 +9,7 @@ from typing import List, Dict, Any, Optional
 
 from src import ai_client
 from src import mcp_client
-from src import models
+from src.mcp_client import RAGConfig
 from src.mcp_client          import RAGConfig
 from src.result_types       import ErrorInfo, ErrorKind, NilRAGState, Result
 from src.type_aliases       import Metadata