To avoid duplication of code and inconsistencies in the database schema, db_tools should be used in create_schema_files. Any additional logic that create_schema_files still contains should be moved to db_tools. Some db_tools function will have to be adjusted, e.g. create_table in db_tools currently doesn't insert indexes into the CREATE TABLE statement but just runs ALTER TABLE queries after the table is created to add them.
The schema files generated after this should be identical to the current ones.