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/models.py

@@ -1,5 +1,5 @@
 """
-Models - legacy Metadata alias only.
+Models - Pydantic proxies + Metadata alias only.
 
 Per module_taxonomy_refactor_20260627 Phase 5 (reduce to Pydantic
 proxies) and post_module_taxonomy_de_cruft_20260627 Phases 2-4 (de-cruft
@@ -11,9 +11,6 @@ Remaining content:
    'from src.models import Metadata' expecting the dataclass
  - The PROVIDERS lazy __getattr__ (loads from src.ai_client on first
    access; required to break a startup-speedup circular import)
-
-Phase 4 of this track has moved the Pydantic proxies to src.api_hooks.py.
-The file is now ~40 lines.
 """
 from __future__ import annotations