The preliminary options and arguments returned from
`.parse_preliminary_options_and_args()` are now all threaded through to
the appropriate methods during initialization.
The configuration file and boolean to ignore configuration files can be
threaded through now that `.parse_preliminary_options_and_args()`
returns options and arguments.
Now that `.parse_preliminary_options_and_args()` returns options and
arguments, the boolean for appending configuration and the arguments can
be threaded through to the creation of the `ConfigFileFinder`.
The verbosity and output file options can be obtained from options
returned by `.parse_preliminary_options_and_args()`, instead of state
from the `Application` object.
