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.

docs/type_registry/src_mcp_client.md

@@ -5,7 +5,7 @@ Auto-generated from source. 4 struct(s) defined in this module.
 ## `src\mcp_client.py::MCPConfiguration`
 
 **Kind:** `dataclass`
-**Defined at:** line 112
+**Defined at:** line 111
 
 **Fields:**
 - `mcpServers: Dict[str, MCPServerConfig]`
@@ -14,7 +14,7 @@ Auto-generated from source. 4 struct(s) defined in this module.
 ## `src\mcp_client.py::MCPServerConfig`
 
 **Kind:** `dataclass`
-**Defined at:** line 86
+**Defined at:** line 85
 
 **Fields:**
 - `name: str`
@@ -27,7 +27,7 @@ Auto-generated from source. 4 struct(s) defined in this module.
 ## `src\mcp_client.py::RAGConfig`
 
 **Kind:** `dataclass`
-**Defined at:** line 157
+**Defined at:** line 156
 
 **Fields:**
 - `enabled: bool`
@@ -40,7 +40,7 @@ Auto-generated from source. 4 struct(s) defined in this module.
 ## `src\mcp_client.py::VectorStoreConfig`
 
 **Kind:** `dataclass`
-**Defined at:** line 126
+**Defined at:** line 125
 
 **Fields:**
 - `provider: str`