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/assistant/__init__.py

@@ -1,11 +1,11 @@
 # #region AssistantApi [C:5] [TYPE Module] [SEMANTICS api, assistant, chat, command, confirmation]
 # @BRIEF API routes for LLM assistant command parsing and safe execution orchestration.
-# @LAYER API
-# @INVARIANT Risky operations are never executed without valid confirmation token.
+# @LAYER: API
 # @RELATION DEPENDS_ON -> [TaskManager]
 # @RELATION DEPENDS_ON -> [AssistantMessageRecord]
 # @RELATION DEPENDS_ON -> [AssistantConfirmationRecord]
 # @RELATION DEPENDS_ON -> [AssistantAuditRecord]
+# @INVARIANT: Risky operations are never executed without valid confirmation token.
 
 # Re-export public API for backward compatibility.
 from ._routes import router, send_message, confirm_operation, cancel_operation