fix: test assertions for molecular CoT markers, separate propagate=False to ConfigManager, fix ruff in env.py

backend/alembic/env.py

@@ -1,3 +1,12 @@
+# #region AlembicEnvModule [C:3] [TYPE Module] [SEMANTICS alembic, migration, env, logging]
+# @BRIEF Alembic environment configuration — sets up DB connection, model metadata,
+#   and logging. Contains ADR [LOG-001] for suppress_existing_loggers=False.
+# @LAYER Infrastructure
+# @RELATION DEPENDS_ON -> [LoggerModule]
+# @INVARIANT fileConfig() must be called with disable_existing_loggers=False
+#   to prevent disabling superset_tools_app logger (see ADR LOG-001).
+# #endregion AlembicEnvModule
+
 from logging.config import fileConfig
 import os
 from pathlib import Path
@@ -38,7 +47,7 @@ if config.config_file_name is not None:
 # add your model's MetaData object here
 # for 'autogenerate' support
 # Import ALL model modules so their tables are registered in Base.metadata
-from src.models import (  # noqa: F401
+from src.models import (  # noqa: F401, E402
     api_key,
     assistant,
     auth,
@@ -57,8 +66,8 @@ from src.models import (  # noqa: F401
 )
 
 # Import config models with explicit alias to avoid name collision with alembic config
-import src.models.config as models_config  # noqa: F401
-from src.models.mapping import Base
+import src.models.config as models_config  # noqa: F401, E402
+from src.models.mapping import Base  # noqa: E402
 
 target_metadata = Base.metadata
 

backend/alembic/versions/2df63b7ce038_add_missing_columns_policy_id_provider_.py

@@ -13,17 +13,17 @@ Revises: 86c7b1d6a710
 Create Date: 2026-05-27 11:17:26.789634
 
 """
-from typing import Sequence, Union
+from collections.abc import Sequence
 
-from alembic import op
 import sqlalchemy as sa
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision: str = '2df63b7ce038'
-down_revision: Union[str, Sequence[str], None] = '86c7b1d6a710'
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
+down_revision: str | Sequence[str] | None = '86c7b1d6a710'
+branch_labels: str | Sequence[str] | None = None
+depends_on: str | Sequence[str] | None = None
 
 
 def upgrade() -> None: