Handle repeated --quiet options again

*Description of changes*

Handle `-q`/`--quiet` again.

*Related to:*  #180

See merge request !89

Fundamentally on Flake8 2.x using -q altered the format of the errors
(and the behaviour a little) so it makes the most sense to implement
this logic with formatters rather than messy logic spread throughout
the project.

The FilenameOnly formatter will keep track of filenames already reported
and only print the name once while Nothing will print nothing.

Closes #180

Wire-up --statistics again

*Description of changes*

Make `--statistics` work again

*Related to:*  #180

See merge request !87

I'm not sure where this code went or when, but it disappeared. Let's
add it back.

Related #180

Without calling start and stop, our output file is not used by our
Formatters and any formatting plugins.

Related #180

If a user specified `--max-complexity` on the command-line, they
would be told that it did not exist. The same would be true of any
option provided by a plugin. This is because we parse the command-line
arguments twice in Flake8 -- the first time to specify the verbosity
and destination for logging, the second time to actually execute Flake8.
Since plugin options are not registered to start with the first time,
they are not valid options. So when we first parse the options, we should
only attempt to parse the ones which we know about.

Closes #168

We need to initialize part of the Application so we can set options
passed by the user, but we also want to delay making things, e.g.,

- Formatter
- Style Guide
- etc.

Until we have the options solidified so we don't have to do annoying
things.

This does not handle setting custom options via the parameters to
get_style_guide.