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/api/config/__init__.py

@@ -0,0 +1 @@
+"""Config module."""

apps/api/src/api/config_profiles.py

@@ -14,10 +14,10 @@ from sqlalchemy.orm import selectinload
 
 from src.api.shared_validators import validate_env_vars as _validate_env_vars
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.config_profile import ConfigProfile, ConfigProfileInclude
+from src.models import ConfigProfile, ConfigProfileInclude
 from src.models.project import Project
-from src.models.tool_type import ToolType
-from src.models.user_config import UserConfig
+from src.models import ToolType
+from src.models import UserConfig
 from src.services.config_profile_resolver import (
     ConfigProfileCycleError,
     check_include_cycle,
@@ -991,7 +991,7 @@ async def validate_git_url(
     env = None
     key_path = None
     if data.ssh_key_id:
-        from src.models.ssh_key import SSHKey
+        from src.models import SSHKey
         from src.services.ssh_keys import _get_fernet
 
         try:

apps/api/src/api/dashboard.py

@@ -5,9 +5,9 @@ from sqlalchemy import func, select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 
 router = APIRouter(prefix="/dashboard", tags=["dashboard"])
 

apps/api/src/api/git_repositories.py

@@ -17,8 +17,8 @@ from src.auth.dependencies import (
     get_db_session,
 )
 from src.config import Settings
-from src.models.git_repository import GitRepository
-from src.models.ssh_key import SSHKey
+from src.models import GitRepository
+from src.models import SSHKey
 from src.utils.git_files import (
     commit_file,
     get_file_content,

apps/api/src/api/instance_proxy.py

@@ -8,8 +8,8 @@ from fastapi import APIRouter, Depends, HTTPException, Request, Response, status
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import ToolInstance
+from src.models import ToolType
 
 logger = logging.getLogger(__name__)
 

apps/api/src/api/notifications.py

@@ -9,7 +9,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user, get_db_session
 from src.models.user import User
-from src.models.user_config import UserConfig
+from src.models import UserConfig
 from src.services.notification_service import notification_service
 
 router = APIRouter(prefix="/notifications", tags=["notifications"])

apps/api/src/api/project/__init__.py

@@ -0,0 +1 @@
+"""Project module."""

apps/api/src/api/projects.py

@@ -13,10 +13,10 @@ from src.auth.dependencies import (
     get_current_user_id,
     get_db_session,
 )
-from src.models.git_repository import GitRepository
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.tool_instance import ToolInstance
+from src.models import SSHKey
+from src.models import ToolInstance
 
 router = APIRouter(prefix="/projects", tags=["projects"])
 
@@ -101,7 +101,7 @@ async def list_projects(
     )
     projects = result.scalars().all()
 
-    from src.models.workspace import Workspace
+    from src.models import Workspace
 
     enriched = []
     for project in projects:

apps/api/src/api/ssh_keys.py

@@ -12,7 +12,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
 from src.config import Settings
-from src.models.ssh_key import SSHKey
+from src.models import SSHKey
 
 router = APIRouter(prefix="/ssh-keys", tags=["ssh-keys"])
 

apps/api/src/api/system/__init__.py

@@ -0,0 +1 @@
+"""System module."""

apps/api/src/api/terminal.py

@@ -12,9 +12,9 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from starlette.websockets import WebSocketDisconnect
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.terminal_session import TerminalSessionModel
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import TerminalSessionModel
+from src.models import ToolInstance
+from src.models import ToolType
 from src.services.terminal_manager import MaxSessionsExceededError, terminal_manager
 
 router = APIRouter()

apps/api/src/api/tool/__init__.py

@@ -0,0 +1 @@
+"""Tool module."""

apps/api/src/api/tool_definitions.py

@@ -9,8 +9,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_definition_manifest import ToolDefinitionManifest
-from src.models.tool_type import ToolType
+from src.models import ToolDefinitionManifest
+from src.models import ToolType
 from src.services.manifest_compiler import (
     compile_compose,
     compile_dockerfile,

apps/api/src/api/tool_instances.py

@@ -30,12 +30,12 @@ from src.auth.dependencies import (
 )
 from src.services.event_bus import InstanceEventBus
 from src.services.lifecycle_hooks import publish_lifecycle_event
-from src.models.config_profile import ConfigProfile
-from src.models.git_repository import GitRepository
+from src.models import ConfigProfile
+from src.models import GitRepository
 from src.models.project import Project
-from src.models.ssh_key import SSHKey
-from src.models.tool_instance import ToolInstance
-from src.models.tool_type import ToolType
+from src.models import SSHKey
+from src.models import ToolInstance
+from src.models import ToolType
 from src.services.clone import check_dirty_state, clone_repository
 from src.services.config_profile_resolver import (
     ConfigProfileCycleError,
@@ -856,7 +856,7 @@ async def create_instance(
     workspace = None
     workspace_id = None
     if data.workspace_id:
-        from src.models.workspace import Workspace as WorkspaceModel
+        from src.models import Workspace as WorkspaceModel
 
         try:
             workspace_id = uuid.UUID(data.workspace_id)
@@ -1056,7 +1056,7 @@ services:
 
         elif tool_type.definition_type == "manifest":
             # Manifest-based: generate compose only; image built lazily on start
-            from src.models.tool_definition_manifest import ToolDefinitionManifest
+            from src.models import ToolDefinitionManifest
 
             manifest_def = await session.get(
                 ToolDefinitionManifest, tool_type.manifest_id
@@ -1341,7 +1341,7 @@ async def _prepare_manifest_instance(
     Returns:
         Tuple of (image_tag, compose_content, resolved_manifest, home_dir)
     """
-    from src.models.tool_definition_manifest import ToolDefinitionManifest
+    from src.models import ToolDefinitionManifest
 
     tool_type = await session.get(ToolType, instance.tool_type_id)
     manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
@@ -1537,7 +1537,7 @@ async def start_instance(
     container_uid = 0
     container_gid = 0
     if tool_type and tool_type.definition_type == "manifest" and tool_type.manifest_id:
-        from src.models.tool_definition_manifest import ToolDefinitionManifest
+        from src.models import ToolDefinitionManifest
 
         manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
         if manifest_def:
@@ -1724,7 +1724,7 @@ async def start_instance(
         # Determine repo path (workspace takes precedence)
         repo_path = ""
         if instance.workspace_id:
-            from src.models.workspace import Workspace as WorkspaceModel
+            from src.models import Workspace as WorkspaceModel
 
             workspace = await session.get(WorkspaceModel, instance.workspace_id)
             if workspace:
@@ -2767,7 +2767,7 @@ async def get_instance_events(
         List of event dictionaries.
     """
     from sqlalchemy import select
-    from src.models.instance_event import InstanceEvent
+    from src.models import InstanceEvent
 
     _user = await _get_user(session, user_id)
     _project = await _get_owned_project(project_id, user_id, session)

apps/api/src/api/tool_types.py

@@ -12,7 +12,7 @@ from src.api.tool_types_validation import (
     validate_required_variables,
 )
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.tool_type import ToolType
+from src.models import ToolType
 from src.models.user import User
 
 router = APIRouter(prefix="/tool-types", tags=["tool-types"])

apps/api/src/api/user/__init__.py

@@ -0,0 +1 @@
+"""User module."""

apps/api/src/api/user_config.py

@@ -7,7 +7,7 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import _get_user, get_current_user_id, get_db_session
-from src.models.user_config import UserConfig
+from src.models import UserConfig
 
 logger = logging.getLogger(__name__)
 

apps/api/src/api/workspace/__init__.py

@@ -0,0 +1 @@
+"""Workspace module."""

apps/api/src/api/workspace_files.py

@@ -6,7 +6,7 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
 from src.services.file_service import FileService
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/files")

apps/api/src/api/workspace_git.py

@@ -6,7 +6,7 @@ from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.workspace import Workspace
+from src.models import Workspace
 from src.services.git_operations import GitOperations
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/git")

apps/api/src/api/workspace_instances.py

@@ -7,8 +7,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.tool_instance import ToolInstance
-from src.models.workspace import Workspace
+from src.models import ToolInstance
+from src.models import Workspace
 
 router = APIRouter(prefix="/workspaces/{workspace_id}/instances")
 

apps/api/src/api/workspaces.py

@@ -9,9 +9,9 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 
 from src.auth.dependencies import get_current_user_id, get_db_session
-from src.models.git_repository import GitRepository
-from src.models.tool_instance import ToolInstance
-from src.models.workspace import Workspace
+from src.models import GitRepository
+from src.models import ToolInstance
+from src.models import Workspace
 from src.services.workspace_manager import WorkspaceHasInstancesError, WorkspaceManager
 
 logger = logging.getLogger(__name__)