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/api/routes/git/_helpers.py

@@ -1,6 +1,6 @@
 # #region GitHelpers [C:3] [TYPE Module] [SEMANTICS git, helpers, resolution, identity]
 # @BRIEF Shared helper functions for Git route modules.
-# @LAYER API
+# @LAYER: API
 # @RELATION USES -> [GitDeps]
 # @RELATION USES -> [SupersetClient]
 # @RELATION USES -> [UserDashboardPreference]
@@ -11,9 +11,7 @@ from typing import Optional
 from fastapi import HTTPException
 from sqlalchemy.orm import Session
 
-from src.core.cot_logger import MarkerLogger
-
-log = MarkerLogger("GitHelpers")
+from src.core.logger import logger
 from src.core.superset_client import SupersetClient
 from src.dependencies import get_config_manager
 from src.models.auth import User
@@ -25,7 +23,7 @@ from ._deps import get_git_service, MAX_REPOSITORY_STATUS_BATCH
 
 # #region _build_no_repo_status_payload [C:1] [TYPE Function]
 # @BRIEF Build a consistent status payload for dashboards without initialized repositories.
-# @POST Returns a stable payload compatible with frontend repository status parsing.
+# @POST: Returns a stable payload compatible with frontend repository status parsing.
 def _build_no_repo_status_payload() -> dict:
     return {
         "is_dirty": False,
@@ -47,24 +45,24 @@ def _build_no_repo_status_payload() -> dict:
 
 # #region _handle_unexpected_git_route_error [C:1] [TYPE Function]
 # @BRIEF Convert unexpected route-level exceptions to stable 500 API responses.
-# @PRE `error` is a non-HTTPException instance.
-# @POST Raises HTTPException(500) with route-specific context.
+# @PRE: `error` is a non-HTTPException instance.
+# @POST: Raises HTTPException(500) with route-specific context.
 def _handle_unexpected_git_route_error(route_name: str, error: Exception) -> None:
-    log.explore(f"{route_name} failed: {error}", error=str(error))
+    logger.error(f"[{route_name}][Coherence:Failed] {error}")
     raise HTTPException(status_code=500, detail=f"{route_name} failed: {str(error)}")
 # #endregion _handle_unexpected_git_route_error
 
 
 # #region _resolve_repository_status [C:2] [TYPE Function]
 # @BRIEF Resolve repository status for one dashboard with graceful NO_REPO semantics.
-# @PRE `dashboard_id` is a valid integer.
-# @POST Returns standard status payload or `NO_REPO` payload when repository path is absent.
+# @PRE: `dashboard_id` is a valid integer.
+# @POST: Returns standard status payload or `NO_REPO` payload when repository path is absent.
 def _resolve_repository_status(dashboard_id: int) -> dict:
     git_service = get_git_service()
     repo_path = git_service._get_repo_path(dashboard_id)
     if not os.path.exists(repo_path):
-        log.reason(
-            f"Repository is not initialized for dashboard {dashboard_id}"
+        logger.debug(
+            f"[get_repository_status][Action] Repository is not initialized for dashboard {dashboard_id}"
         )
         return _build_no_repo_status_payload()
 
@@ -72,8 +70,8 @@ def _resolve_repository_status(dashboard_id: int) -> dict:
         return git_service.get_status(dashboard_id)
     except HTTPException as e:
         if e.status_code == 404:
-            log.reason(
-                f"Repository is not initialized for dashboard {dashboard_id}"
+            logger.debug(
+                f"[get_repository_status][Action] Repository is not initialized for dashboard {dashboard_id}"
             )
             return _build_no_repo_status_payload()
         raise
@@ -289,7 +287,11 @@ def _resolve_current_user_git_identity(
             .first()
         )
     except Exception as resolve_error:
-        log.explore(f"Failed to load profile preference for user {user_id}: {resolve_error}", error=str(resolve_error))
+        logger.warning(
+            "[_resolve_current_user_git_identity][Action] Failed to load profile preference for user %s: %s",
+            user_id,
+            resolve_error,
+        )
         return None
 
     if not preference: