refactor: reorganize models into subpackages

Move models into domain subpackages (max 4 files each):
- models/tool/ — tool_type, tool_instance, tool_definition_manifest
- models/config/ — config_profile
- models/user/ — user, user_config, ssh_key
- models/project/ — project, git_repository, workspace
- models/system/ — health_check, notification, instance_event, terminal_session

models/__init__.py continues to re-export all symbols, so consumers
using 'from src.models import X' are unaffected. Updated direct file
imports across the backend to use the new paths.

Quality gates: py_compile passed, ruff passed.

apps/api/src/services/health_monitor.py

@@ -10,8 +10,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.database import SessionLocal
-from src.models.health_check import HealthCheck
-from src.models.tool_instance import ToolInstance
+from src.models import HealthCheck
+from src.models import ToolInstance
 from src.services.correlation import get_correlation_id
 from src.services.docker import get_container_status
 from src.services.tunnel import check_tunnel_health