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/core/plugin_loader.py

@@ -7,7 +7,7 @@ from .logger import belief_scope
 
 # #region PluginLoader [C:3] [TYPE Class] [SEMANTICS plugin, loader, dynamic, import]
 # @BRIEF Scans a specified directory for Python modules, dynamically loads them, and registers any classes that are valid implementations of the PluginBase interface.
-# @LAYER Core
+# @LAYER: Core
 # @RELATION Depends on PluginBase. It is used by the main application to discover and manage available plugins.
 class PluginLoader:
     """
@@ -15,10 +15,10 @@ class PluginLoader:
     that inherit from PluginBase.
     """
 
-    # #region __init__ [TYPE Function]
-    # @BRIEF Initializes the PluginLoader with a directory to scan.
-    # @PRE plugin_dir is a valid directory path.
-    # @POST Plugins are loaded and registered.
+    # [DEF:__init__:Function]
+    # @PURPOSE: Initializes the PluginLoader with a directory to scan.
+    # @PRE:     plugin_dir is a valid directory path.
+    # @POST:    Plugins are loaded and registered.
     # @PARAM: plugin_dir (str) - The directory containing plugin modules.
     def __init__(self, plugin_dir: str):
         with belief_scope("__init__"):
@@ -26,12 +26,12 @@ class PluginLoader:
             self._plugins: Dict[str, PluginBase] = {}
             self._plugin_configs: Dict[str, PluginConfig] = {}
             self._load_plugins()
-    # #endregion __init__
+    # [/DEF:__init__:Function]
 
-    # #region _load_plugins [TYPE Function]
-    # @BRIEF Scans the plugin directory and loads all valid plugins.
-    # @PRE plugin_dir exists or can be created.
-    # @POST _load_module is called for each .py file.
+    # [DEF:_load_plugins:Function]
+    # @PURPOSE: Scans the plugin directory and loads all valid plugins.
+    # @PRE:     plugin_dir exists or can be created.
+    # @POST:    _load_module is called for each .py file.
     def _load_plugins(self):
         with belief_scope("_load_plugins"):
             """
@@ -61,12 +61,12 @@ class PluginLoader:
             if filename.endswith(".py") and filename != "__init__.py":
                 module_name = filename[:-3]
                 self._load_module(module_name, file_path)
-    # #endregion _load_plugins
+    # [/DEF:_load_plugins:Function]
 
-    # #region _load_module [TYPE Function]
-    # @BRIEF Loads a single Python module and discovers PluginBase implementations.
-    # @PRE module_name and file_path are valid.
-    # @POST Plugin classes are instantiated and registered.
+    # [DEF:_load_module:Function]
+    # @PURPOSE: Loads a single Python module and discovers PluginBase implementations.
+    # @PRE:     module_name and file_path are valid.
+    # @POST:    Plugin classes are instantiated and registered.
     # @PARAM: module_name (str) - The name of the module.
     # @PARAM: file_path (str) - The path to the module file.
     def _load_module(self, module_name: str, file_path: str):
@@ -102,12 +102,12 @@ class PluginLoader:
                     self._register_plugin(plugin_instance)
                 except Exception as e:
                     print(f"Error instantiating plugin {attribute_name} in {module_name}: {e}") # Replace with proper logging
-    # #endregion _load_module
+    # [/DEF:_load_module:Function]
 
-    # #region _register_plugin [TYPE Function]
-    # @BRIEF Registers a PluginBase instance and its configuration.
-    # @PRE plugin_instance is a valid implementation of PluginBase.
-    # @POST Plugin is added to _plugins and _plugin_configs.
+    # [DEF:_register_plugin:Function]
+    # @PURPOSE: Registers a PluginBase instance and its configuration.
+    # @PRE:     plugin_instance is a valid implementation of PluginBase.
+    # @POST:    Plugin is added to _plugins and _plugin_configs.
     # @PARAM: plugin_instance (PluginBase) - The plugin instance to register.
     def _register_plugin(self, plugin_instance: PluginBase):
         with belief_scope("_register_plugin"):
@@ -143,13 +143,13 @@ class PluginLoader:
         except Exception as e:
             from ..core.logger import logger
             logger.error(f"Error validating plugin '{plugin_instance.name}' (ID: {plugin_id}): {e}")
-    # #endregion _register_plugin
+    # [/DEF:_register_plugin:Function]
 
 
-    # #region get_plugin [TYPE Function]
-    # @BRIEF Retrieves a loaded plugin instance by its ID.
-    # @PRE plugin_id is a string.
-    # @POST Returns plugin instance or None.
+    # [DEF:get_plugin:Function]
+    # @PURPOSE: Retrieves a loaded plugin instance by its ID.
+    # @PRE:     plugin_id is a string.
+    # @POST:    Returns plugin instance or None.
     # @PARAM: plugin_id (str) - The unique identifier of the plugin.
     # @RETURN: Optional[PluginBase] - The plugin instance if found, otherwise None.
     def get_plugin(self, plugin_id: str) -> Optional[PluginBase]:
@@ -158,25 +158,25 @@ class PluginLoader:
             Returns a loaded plugin instance by its ID.
             """
         return self._plugins.get(plugin_id)
-    # #endregion get_plugin
+    # [/DEF:get_plugin:Function]
 
-    # #region get_all_plugin_configs [TYPE Function]
-    # @BRIEF Returns a list of all registered plugin configurations.
-    # @PRE None.
-    # @POST Returns list of all PluginConfig objects.
-    # @RETURN List[PluginConfig] - A list of plugin configurations.
+    # [DEF:get_all_plugin_configs:Function]
+    # @PURPOSE: Returns a list of all registered plugin configurations.
+    # @PRE:     None.
+    # @POST:    Returns list of all PluginConfig objects.
+    # @RETURN: List[PluginConfig] - A list of plugin configurations.
     def get_all_plugin_configs(self) -> List[PluginConfig]:
         with belief_scope("get_all_plugin_configs"):
             """
             Returns a list of all loaded plugin configurations.
             """
         return list(self._plugin_configs.values())
-    # #endregion get_all_plugin_configs
+    # [/DEF:get_all_plugin_configs:Function]
 
-    # #region has_plugin [TYPE Function]
-    # @BRIEF Checks if a plugin with the given ID is registered.
-    # @PRE plugin_id is a string.
-    # @POST Returns True if plugin exists.
+    # [DEF:has_plugin:Function]
+    # @PURPOSE: Checks if a plugin with the given ID is registered.
+    # @PRE:     plugin_id is a string.
+    # @POST:    Returns True if plugin exists.
     # @PARAM: plugin_id (str) - The unique identifier of the plugin.
     # @RETURN: bool - True if the plugin is registered, False otherwise.
     def has_plugin(self, plugin_id: str) -> bool:
@@ -185,6 +185,6 @@ class PluginLoader:
             Checks if a plugin with the given ID is loaded.
             """
         return plugin_id in self._plugins
-    # #endregion has_plugin
+    # [/DEF:has_plugin:Function]
 
 # #endregion PluginLoader