feat: workspace-first UI refresh - PR-1 backend endpoints

- Add FileService for workspace-scoped file operations
- Add GitOperations service for workspace-scoped git commands
- Add workspace_files API: GET/POST /workspaces/{id}/files
- Add workspace_git API: status, branches, commit, push, pull, fetch, checkout, history
- Add workspace_instances API: list instances per workspace
- Add top-level POST /workspaces/ (accepts repo_id directly)
- Enrich GET /projects/ with nested repositories and workspaces
- Register all new routers in main.py
- 23 tests passing (17 existing + 6 new)

Quality gates: ruff clean

apps/api/src/main.py

@@ -24,6 +24,9 @@ from src.api.tool_types import router as tool_types_router
 from src.api.notifications import router as notifications_router
 from src.api.user_config import router as user_config_router
 from src.api.users import router as users_router
+from src.api.workspace_files import router as workspace_files_router
+from src.api.workspace_git import router as workspace_git_router
+from src.api.workspace_instances import router as workspace_instances_router
 from src.api.workspaces import all_workspaces_router, router as workspaces_router
 from src.config import Settings
 from src.models.notification import Notification  # noqa: F401 – Alembic model discovery
@@ -162,4 +165,7 @@ app.include_router(events_router)
 app.include_router(notifications_router)
 app.include_router(all_workspaces_router)
 app.include_router(workspaces_router)
+app.include_router(workspace_files_router)
+app.include_router(workspace_git_router)
+app.include_router(workspace_instances_router)
 app.mount("/uploads", StaticFiles(directory="uploads"), name="uploads")