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/project_manager.py

@@ -193,7 +193,7 @@ def load_project(path: Union[str, Path]) -> Metadata:
  with open(path, "rb") as f: proj = tomllib.load(f)
  # Deserialise FileItems in files.paths
  if "files" in proj and "paths" in proj["files"]:
-  from src import models
+  from src.project_files import FileItem
   proj["files"]["paths"] = [FileItem.from_dict(p) if isinstance(p, dict) else p for p in proj["files"]["paths"]]
  hist_path = get_history_path(path)
  if "discussion" in proj: