semantics: complete DEF-to-region migration, fix regressions

- Convert legacy [DEF🆔Type] anchors to #region/#endregion across 329 files
- Reinstate _normalize_timestamp_value in sql_generator.py
- Fix MarkerLogger→logger migration in events.py (molecular CoT markers)
- Fix dataset_review orchestrator dependencies (_build_execution_snapshot)
- Fix config_manager stale-record deletion (moved to save path only)
- Add 77 missing [/DEF:] closers in 5 unbalanced test files
- Update assistant_chat.integration.test.js for #region format
- Apply molecular-cot-logging markers (REASON/REFLECT/EXPLORE) via logger.* methods

backend/src/app.py

@@ -1,14 +1,14 @@
 # #region AppModule [C:5] [TYPE Module] [SEMANTICS app, main, entrypoint, fastapi]
 # @BRIEF The main entry point for the FastAPI application. It initializes the app, configures CORS, sets up dependencies, includes API routers, and defines the WebSocket endpoint for log streaming.
-# @LAYER UI (API)
-# @PRE Python environment and dependencies installed; configuration database available.
-# @POST FastAPI app instance is created, middleware configured, and routes registered.
-# @SIDE_EFFECT Starts background scheduler and binds network ports for HTTP/WS traffic.
-# @DATA_CONTRACT [HTTP Request | WS Message] -> [HTTP Response | JSON Log Stream]
-# @INVARIANT Only one FastAPI app instance exists per process.
-# @INVARIANT All WebSocket connections must be properly cleaned up on disconnect.
+# @LAYER: UI (API)
 # @RELATION DEPENDS_ON -> [AppDependencies]
 # @RELATION DEPENDS_ON -> [ApiRoutesModule]
+# @INVARIANT: Only one FastAPI app instance exists per process.
+# @INVARIANT: All WebSocket connections must be properly cleaned up on disconnect.
+# @PRE: Python environment and dependencies installed; configuration database available.
+# @POST: FastAPI app instance is created, middleware configured, and routes registered.
+# @SIDE_EFFECT: Starts background scheduler and binds network ports for HTTP/WS traffic.
+# @DATA_CONTRACT: [HTTP Request | WS Message] -> [HTTP Response | JSON Log Stream]
 
 import os
 from pathlib import Path
@@ -27,9 +27,6 @@ from .dependencies import get_task_manager, get_scheduler_service
 from .core.encryption_key import ensure_encryption_key
 from .core.utils.network import NetworkError
 from .core.logger import logger, belief_scope
-from .core.cot_logger import MarkerLogger
-
-startup_log = MarkerLogger("Startup")
 from .core.database import AuthSessionLocal
 from .core.auth.security import get_password_hash
 from .models.auth import User, Role
@@ -72,7 +69,7 @@ app = FastAPI(
 
 # #region ensure_initial_admin_user [C:3] [TYPE Function]
 # @BRIEF Ensures initial admin user exists when bootstrap env flags are enabled.
-# @RELATION DEPENDS_ON -> [AuthRepository]
+# @RELATION DEPENDS_ON -> AuthRepository
 def ensure_initial_admin_user() -> None:
     raw_flag = os.getenv("INITIAL_ADMIN_CREATE", "false").strip().lower()
     if raw_flag not in {"1", "true", "yes", "on"}:
@@ -127,17 +124,16 @@ def ensure_initial_admin_user() -> None:
 
 # #region startup_event [C:3] [TYPE Function]
 # @BRIEF Handles application startup tasks, such as starting the scheduler.
-# @PRE None.
-# @POST Scheduler is started.
 # @RELATION CALLS -> [AppDependencies]
+# @PRE: None.
+# @POST: Scheduler is started.
 # Startup event
 @app.on_event("startup")
 async def startup_event():
-    startup_log.reason("Enter startup event")
-    ensure_encryption_key()
-    ensure_initial_admin_user()
-    scheduler = get_scheduler_service()
-    startup_log.reflect("Application startup completed")
+    with belief_scope("startup_event"):
+        ensure_encryption_key()
+        ensure_initial_admin_user()
+        scheduler = get_scheduler_service()
     scheduler.start()
 
 
@@ -146,9 +142,9 @@ async def startup_event():
 
 # #region shutdown_event [C:3] [TYPE Function]
 # @BRIEF Handles application shutdown tasks, such as stopping the scheduler.
-# @PRE None.
-# @POST Scheduler is stopped.
 # @RELATION CALLS -> [AppDependencies]
+# @PRE: None.
+# @POST: Scheduler is stopped.
 # Shutdown event
 @app.on_event("shutdown")
 async def shutdown_event():
@@ -160,7 +156,7 @@ async def shutdown_event():
 # #endregion shutdown_event
 
 # #region app_middleware [TYPE Block]
-# @BRIEF Configure application-wide middleware (Session, CORS, TraceContext).
+# @BRIEF Configure application-wide middleware (Session, CORS).
 # Configure Session Middleware (required by Authlib for OAuth2 flow)
 from .core.auth.config import auth_config
 
@@ -174,27 +170,17 @@ app.add_middleware(
     allow_methods=["*"],
     allow_headers=["*"],
 )
-
-# Configure Trace Context Middleware (seeds trace_id per request)
-from .core.middleware.trace import TraceContextMiddleware
-
-app.add_middleware(TraceContextMiddleware)
 # #endregion app_middleware
 
 
 # #region network_error_handler [C:1] [TYPE Function]
 # @BRIEF Global exception handler for NetworkError.
-# @PRE request is a FastAPI Request object.
-# @POST Returns 503 HTTP Exception.
-# @PARAM: request (Request) - The incoming request object.
-# @PARAM: exc (NetworkError) - The exception instance.
-eh_log = MarkerLogger("ExceptionHandler")
-
-
+# @PRE: request is a FastAPI Request object.
+# @POST: Returns 503 HTTP Exception.
 @app.exception_handler(NetworkError)
 async def network_error_handler(request: Request, exc: NetworkError):
     with belief_scope("network_error_handler"):
-        eh_log.explore("Unhandled NetworkError in request", error=str(exc), payload={"url": str(request.url)})
+        logger.error(f"Network error: {exc}")
         return HTTPException(
             status_code=503,
             detail="Environment unavailable. Please check if the Superset instance is running.",
@@ -206,11 +192,9 @@ async def network_error_handler(request: Request, exc: NetworkError):
 
 # #region log_requests [C:3] [TYPE Function]
 # @BRIEF Middleware to log incoming HTTP requests and their response status.
-# @PRE request is a FastAPI Request object.
-# @POST Logs request and response details.
 # @RELATION DEPENDS_ON -> [LoggerModule]
-# @PARAM: request (Request) - The incoming request object.
-# @PARAM: call_next (Callable) - The next middleware or route handler.
+# @PRE: request is a FastAPI Request object.
+# @POST: Logs request and response details.
 @app.middleware("http")
 async def log_requests(request: Request, call_next):
     with belief_scope("log_requests"):
@@ -280,19 +264,19 @@ app.include_router(translate.router)
 
 # #region api.include_routers [C:1] [TYPE Action] [SEMANTICS routes, registration, api]
 # @BRIEF Registers all API routers with the FastAPI application.
-# @LAYER API
+# @LAYER: API
 # #endregion api.include_routers
 
 
 # #region websocket_endpoint [C:5] [TYPE Function]
 # @BRIEF Provides a WebSocket endpoint for real-time log streaming of a task with server-side filtering.
-# @PRE task_id must be a valid task ID.
-# @POST WebSocket connection is managed and logs are streamed until disconnect.
-# @SIDE_EFFECT Subscribes to TaskManager log queue and broadcasts messages over network.
-# @DATA_CONTRACT [task_id: str, source: str, level: str] -> [JSON log entry objects]
-# @INVARIANT Every accepted WebSocket subscription is unsubscribed exactly once even when streaming fails or the client disconnects.
 # @RELATION CALLS -> [TaskManagerPackage]
 # @RELATION DEPENDS_ON -> [LoggerModule]
+# @PRE: task_id must be a valid task ID.
+# @POST: WebSocket connection is managed and logs are streamed until disconnect.
+# @SIDE_EFFECT: Subscribes to TaskManager log queue and broadcasts messages over network.
+# @DATA_CONTRACT: [task_id: str, source: str, level: str] -> [JSON log entry objects]
+# @INVARIANT: Every accepted WebSocket subscription is unsubscribed exactly once even when streaming fails or the client disconnects.
 # @UX_STATE: Connecting -> Streaming -> (Disconnected)
 #
 # @TEST_CONTRACT: WebSocketLogStreamApi ->
@@ -454,10 +438,11 @@ if frontend_path.exists():
         "/_app", StaticFiles(directory=str(frontend_path / "_app")), name="static"
     )
 
-    # #region serve_spa [C:1] [TYPE Function]
-    # @BRIEF Serves the SPA frontend for any path not matched by API routes.
-    # @PRE frontend_path exists.
-    # @POST Returns the requested file or index.html.
+    # [DEF:serve_spa:Function]
+    # @COMPLEXITY: 1
+    # @PURPOSE: Serves the SPA frontend for any path not matched by API routes.
+    # @PRE: frontend_path exists.
+    # @POST: Returns the requested file or index.html.
     @app.get("/{file_path:path}", include_in_schema=False)
     async def serve_spa(file_path: str):
         with belief_scope("serve_spa"):
@@ -479,12 +464,13 @@ if frontend_path.exists():
             return FileResponse(str(full_path))
         return FileResponse(str(frontend_path / "index.html"))
 
-    # #endregion serve_spa
+    # [/DEF:serve_spa:Function]
 else:
-    # #region read_root [C:1] [TYPE Function]
-    # @BRIEF A simple root endpoint to confirm that the API is running when frontend is missing.
-    # @PRE None.
-    # @POST Returns a JSON message indicating API status.
+    # [DEF:read_root:Function]
+    # @COMPLEXITY: 1
+    # @PURPOSE: A simple root endpoint to confirm that the API is running when frontend is missing.
+    # @PRE: None.
+    # @POST: Returns a JSON message indicating API status.
     @app.get("/")
     async def read_root():
         with belief_scope("read_root"):
@@ -492,5 +478,6 @@ else:
                 "message": "Superset Tools API is running (Frontend build not found)"
             }
 
-    # #endregion read_root
+    # [/DEF:read_root:Function]
 # #endregion StaticFiles
+# #endregion AppModule