Small observation I made during debug using pipenv run darjeeling --debug repair <YML>:
logger.debug messages are only being printed to STDOUT for these modules:
(DEBUG) cement.core.config
(DEBUG) cement.core.extension
(DEBUG) cement.core.foundation
(DEBUG) cement.core.handler
(DEBUG) cement.core.hook
(DEBUG) cement.core.interface
(DEBUG) cement.ext.ext_argparse
(DEBUG) cement.ext.ext_logging