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. This only applies to python files for now.

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.

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.