The command line interface of is modeled as an application via ~flake8.main.cli.Application. When a user runs flake8 at their command line, ~flake8.main.cli.main is run which handles management of the application.
User input is parsed twice to accommodate logging and verbosity options passed by the user as early as possible. This is so as much logging can be produced as possible.
The default options are registered by ~flake8.main.options.register_default_options. Trying to register these options in plugins will result in errors.
flake8.main.cli.main
flake8.main.application.Application
flake8.main.options.register_default_options