reproduce_flake8_bug.py

import flake8
from flake8.formatting import base as formatter
from flake8.main import application as app
import flake8.options.config as config

application = app.Application()

application.parse_preliminary_options_and_args([])
flake8.configure_logging(
        application.prelim_opts.verbose, application.prelim_opts.output_file
    )
application.make_config_finder()
application.find_plugins()
application.register_plugin_options()
application.parse_configuration_and_cli([])

# output differs between Jupyter notebook and Python terminal
print(application.config_finder.local_config_files)

# output is the same between Jupyter notebook and Python terminal
cff = config.ConfigFileFinder(application.program_name, [], [])
print(cff.local_config_files())

See issue on GitLab: https://gitlab.com/pycqa/flake8/issues/518