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.
Looking at the pep8 github repo, I think you're right about it not being very active. I'm not hopeful that your patch will get merged any time soon. I see 3 options:

1. Deal with having crappy really long lines in this config file.
2. Move this setting back to the bash script where it was fairly readable, but would only apply when using our bash script. Which is probably fine.
3. Use a different version of pep8 that has your patch, or one like it, applied. I don't really want to become a maintainer for pep8, but maybe someone else does.
4. Switch to a different linter that is more maintained.