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

If users do `from flake8.api.legacy import *` we only want them to get
get_style_guide imported. The other classes are not meant to be created
by users.

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.

Also refactor our statistics module to be a bit smarter and less
namedtuple happy. The Statistic class had no reason to be a tuple,
I have no clue why I wrote it that way last night.

Some plugins (e.g., flake8-future-import) report errors for empty
files. Those plugins default to reporting the line number as 1 which
caused earlier versions of Flake8 3.0 beta to crash on an IndexError

Closes #157