This fixes a regression introduced in daca2c8 and b14d47b.

The --output-file` option was consumed by the preliminary option parser.
However, the `BaseFormatter` class needs the option for setting the
output filename.  This special cases this option to ensure it gets
re-parsed and respected when specified on the CLI.

Now that `ConfigFileFinder.config_file` attribute is used everywhere and
is constructed from the `--config` CLI option, the now unused
`cli_config` parameters can be safely removed.

The `--config` flag is passed into `MergedConfigParser.parse()` and the
module-level function `config.get_local_plugins()`.  Since both of these
places utilize the `ConfigFileFinder` object and the configuration file
override pertains to how configuration behaves, this incremental change
directly associates the `ConfigFileFinder` and the configuration file
override.

The 'ignore_config_files' parameter was accidentally not removed in
c918e72.

Now that `ConfigFileFinder.ignore_config_files` attribute is used
everywhere and is constructed from the `--isolated` CLI option, the now
unused `isolated` parameters can be safely removed.

The `--isolated` flag is passed into `MergedConfigParser.parse()` and
the module-level function `config.get_local_plugins()`.  Since both of
these places utilize the `ConfigFileFinder` object and isolation
pertains to how the `ConfigFileFinder` should behave with respect to
isolation, this incremental change more directly associates the
`ConfigFileFinder` and configuration file isolate.