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/seeds/builtin_tool_types.py

@@ -5,7 +5,7 @@ import logging
 from sqlalchemy import select, text
 
 from src.database import SessionLocal
-from src.models.tool_type import ToolType
+from src.models import ToolType
 
 logger = logging.getLogger(__name__)