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/scripts/seed_permissions.py

@@ -1,15 +1,14 @@
 # #region SeedPermissionsScript [C:3] [TYPE Module] [SEMANTICS setup, database, auth, permissions, seeding]
+#
 # @BRIEF Populates the auth database with initial system permissions.
-# @LAYER Scripts
-# @INVARIANT Safe to run multiple times (idempotent).
-# @RELATION DEPENDS_ON -> [AuthSessionLocal]
-# @RELATION DEPENDS_ON -> [Permission]
-# @RELATION DEPENDS_ON -> [Role]
-# @RELATION DEPENDS_ON -> [AuthRepository]
-#
+# @LAYER:     Scripts
+# @RELATION DEPENDS_ON -> AuthSessionLocal
+# @RELATION DEPENDS_ON -> Permission
+# @RELATION DEPENDS_ON -> Role
+# @RELATION DEPENDS_ON -> AuthRepository
 #
+# @INVARIANT: Safe to run multiple times (idempotent).
 
-# [SECTION: IMPORTS]
 import sys
 from pathlib import Path
 
@@ -20,11 +19,10 @@ from src.core.database import AuthSessionLocal
 from src.models.auth import Permission, Role
 from src.core.auth.repository import AuthRepository
 from src.core.logger import logger, belief_scope
-# [/SECTION]
 
 # #region INITIAL_PERMISSIONS [C:3] [TYPE Constant]
 # @BRIEF Canonical bootstrap permission tuples seeded into auth storage.
-# @RELATION DEPENDS_ON -> [SeedPermissionsScript]
+# @RELATION DEPENDS_ON -> SeedPermissionsScript
 INITIAL_PERMISSIONS = [
     # Admin Permissions
     {"resource": "admin:users", "action": "READ"},
@@ -61,12 +59,12 @@ INITIAL_PERMISSIONS = [
 
 # #region seed_permissions [C:3] [TYPE Function]
 # @BRIEF Inserts missing permissions into the database.
-# @POST All INITIAL_PERMISSIONS exist in the DB.
-# @RELATION DEPENDS_ON -> [AuthSessionLocal]
-# @RELATION DEPENDS_ON -> [Permission]
-# @RELATION DEPENDS_ON -> [Role]
-# @RELATION DEPENDS_ON -> [AuthRepository]
-# @RELATION DEPENDS_ON -> [INITIAL_PERMISSIONS]
+# @POST:    All INITIAL_PERMISSIONS exist in the DB.
+# @RELATION DEPENDS_ON -> AuthSessionLocal
+# @RELATION DEPENDS_ON -> Permission
+# @RELATION DEPENDS_ON -> Role
+# @RELATION DEPENDS_ON -> AuthRepository
+# @RELATION DEPENDS_ON -> INITIAL_PERMISSIONS
 def seed_permissions():
     with belief_scope("seed_permissions"):
         db = AuthSessionLocal()