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/services/git/_status.py

@@ -1,25 +1,23 @@
 # #region GitServiceStatusMixin [C:3] [TYPE Module] [SEMANTICS git, status, diff, history, porcelain]
+# @LAYER: Infra
 # @BRIEF Status, diff, and commit history operations for GitService using git status --porcelain to avoid --cached flag issues.
-# @LAYER Infra
 # @RELATION USED_BY -> [GitService]
 
 from typing import Any, Dict, List
 from datetime import datetime
 from git import Repo
-from src.core.cot_logger import MarkerLogger
-from src.core.logger import belief_scope
-
-log = MarkerLogger("GitStatus")
+from src.core.logger import logger, belief_scope
 
 
 # #region GitServiceStatusMixin [C:3] [TYPE Class]
 # @BRIEF Mixin providing repository status, diff, and commit history for GitService.
 class GitServiceStatusMixin:
-    # #region _parse_status_porcelain [C:2] [TYPE Function]
-    # @BRIEF Parse git status --porcelain output into staged, modified, and untracked file lists.
-    # @PRE `repo` is an open GitPython Repo instance.
-    # @POST Returns (staged, modified, untracked) tuple of file path lists.
-    # @RATIONALE Avoids repo.is_dirty() / repo.index.diff("HEAD") which internally
+    # [DEF:_parse_status_porcelain:Function]
+    # @COMPLEXITY: 2
+    # @PURPOSE: Parse git status --porcelain output into staged, modified, and untracked file lists.
+    # @PRE: `repo` is an open GitPython Repo instance.
+    # @POST: Returns (staged, modified, untracked) tuple of file path lists.
+    # @RATIONALE: Avoids repo.is_dirty() / repo.index.diff("HEAD") which internally
     #   call git diff --cached, a flag unsupported in some Git environments (exit 129).
     #   Using git status --porcelain is self-contained and avoids the --cached flag entirely.
     def _parse_status_porcelain(self, repo) -> tuple[list[str], list[str], list[str]]:
@@ -30,7 +28,7 @@ class GitServiceStatusMixin:
             try:
                 output = repo.git.status("--porcelain")
             except Exception:
-                log.explore("git status --porcelain failed", error="git status --porcelain command failed")
+                logger.warning("[_parse_status_porcelain][Coherence:Failed] git status --porcelain failed")
                 return staged, modified, untracked
             for line in output.split("\n"):
                 if not line:
@@ -52,13 +50,13 @@ class GitServiceStatusMixin:
                     if path not in modified:
                         modified.append(path)
             return staged, modified, untracked
-    # #endregion _parse_status_porcelain
+    # [/DEF:_parse_status_porcelain:Function]
 
-    # #region get_status [TYPE Function]
-    # @BRIEF Get current repository status (dirty files, untracked, etc.)
-    # @PRE Repository for dashboard_id exists.
-    # @POST Returns a dictionary representing the Git status.
-    # @RETURN dict
+    # [DEF:get_status:Function]
+    # @PURPOSE: Get current repository status (dirty files, untracked, etc.)
+    # @PRE: Repository for dashboard_id exists.
+    # @POST: Returns a dictionary representing the Git status.
+    # @RETURN: dict
     def get_status(self, dashboard_id: int) -> dict:
         with belief_scope("GitService.get_status"):
             repo = self.get_repo(dashboard_id)
@@ -112,10 +110,10 @@ class GitServiceStatusMixin:
                 "is_diverged": is_diverged,
                 "sync_state": sync_state,
             }
-    # #endregion get_status
+    # [/DEF:get_status:Function]
 
-    # #region get_diff [TYPE Function]
-    # @BRIEF Generate diff for a file or the whole repository.
+    # [DEF:get_diff:Function]
+    # @PURPOSE: Generate diff for a file or the whole repository.
     # @PARAM: file_path (str) - Optional specific file.
     # @PARAM: staged (bool) - Whether to show staged changes.
     # @PRE: Repository for dashboard_id exists.
@@ -130,10 +128,10 @@ class GitServiceStatusMixin:
             if file_path:
                 return repo.git.diff(*diff_args, "--", file_path)
             return repo.git.diff(*diff_args)
-    # #endregion get_diff
+    # [/DEF:get_diff:Function]
 
-    # #region get_commit_history [TYPE Function]
-    # @BRIEF Retrieve commit history for a repository.
+    # [DEF:get_commit_history:Function]
+    # @PURPOSE: Retrieve commit history for a repository.
     # @PARAM: limit (int) - Max number of commits to return.
     # @PRE: Repository for dashboard_id exists.
     # @POST: Returns a list of dictionaries for each commit in history.
@@ -155,8 +153,9 @@ class GitServiceStatusMixin:
                         "files_changed": list(commit.stats.files.keys())
                     })
             except Exception as e:
-                log.explore(f"Could not retrieve commit history for dashboard {dashboard_id}: {e}", error=str(e))
+                logger.warning(f"[get_commit_history][Action] Could not retrieve commit history for dashboard {dashboard_id}: {e}")
                 return []
             return commits
-    # #endregion get_commit_history
+    # [/DEF:get_commit_history:Function]
+# #endregion GitServiceStatusMixin
 # #endregion GitServiceStatusMixin