Raise line limit to 99 chars in linter.

A while ago pep8 introduced a controversial change that allowed for lines up to 99 characters long, instead of the traditional 79, in the case that everyone on the project could agree that they liked 99 better.

I think we can all agree on 99 (if I'm wrong, please speak  up). In this PR, I have also convinced the robots to like 99 too. This only applies to Python files.

I also moved the exclude list from the lint script and into the flake8 config file. I think it's better there, even if it looks ugly.
flake8 passes it directly to pep8 which doesn't handle it right for exactly the reasons you theorize:

https://github.com/jcrocholl/pep8/issues/339