refactor: move API routers into domain subpackages

Moves 21 API router files into 6 domain subpackages (max 6 files each):
- api/tool/ — tool_instances, tool_types, tool_definitions, sessions
- api/config/ — config_profiles, user_config
- api/workspace/ — workspaces, workspace_files, workspace_git, workspace_instances
- api/user/ — users, auth, ssh_keys
- api/project/ — projects, git_repositories
- api/system/ — health, events, notifications, dashboard, terminal, instance_proxy

sessions_router extracted from tool_instances.py into tool/sessions.py.

main.py now imports from subpackage __init__.py re-exports.
Cross-router imports updated to use new paths.
Fixed pre-existing E712 in tool_definitions.py (is_base == False → is_(False)).

Quality gates: py_compile passed on all files, ruff passed.

apps/api/src/api/tool/tool_definitions.py

@@ -173,7 +173,7 @@ async def list_tool_definitions(
     """
     query = select(ToolDefinitionManifest)
     if not include_bases:
-        query = query.where(ToolDefinitionManifest.is_base == False)
+        query = query.where(ToolDefinitionManifest.is_base.is_(False))
 
     result = await session.execute(
         query.order_by(ToolDefinitionManifest.created_at.desc())

apps/api/src/api/tool/tool_instances.py

@@ -30,7 +30,6 @@ from src.services.instance.event_bus import InstanceEventBus
 from src.services.instance.lifecycle_hooks import publish_lifecycle_event
 from src.models import ConfigProfile
 from src.models import GitRepository
-from src.models.project import Project
 from src.models import SSHKey
 from src.models import ToolInstance
 from src.models import ToolType