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/models/__init__.py

@@ -1,18 +1,18 @@
 from src.models.base import Base
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
-from src.models.git_repository import GitRepository
-from src.models.health_check import HealthCheck
-from src.models.instance_event import InstanceEvent
-from src.models.notification import Notification
-from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.terminal_session import TerminalSessionModel
-from src.models.tool_definition_manifest import ToolDefinitionManifest
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
-from src.models.user import User
-from src.models.user_config import UserConfig
-from src.models.workspace import Workspace
+from src.models.config.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models.project.git_repository import GitRepository
+from src.models.project.project import Project
+from src.models.project.workspace import Workspace
+from src.models.system.health_check import HealthCheck
+from src.models.system.instance_event import InstanceEvent
+from src.models.system.notification import Notification
+from src.models.system.terminal_session import TerminalSessionModel
+from src.models.tool.tool_definition_manifest import ToolDefinitionManifest
+from src.models.tool.tool_instance import ToolInstance
+from src.models.tool.tool_type import ToolType
+from src.models.user.ssh_key import SSHKey
+from src.models.user.user import User
+from src.models.user.user_config import UserConfig
 
 __all__ = [
     "Base",