Massive pep8/pyflakes cleanup

The pyflakes and pep8 checks should now run automatically when Travis CI builds run. I've documented which flags are ignored in .travis.yml (e.g. line length checks).
This one is, but not all of our migrations are. In fact, I personally prefer manually making the migrations. Even when they are auto-generated, they are by definition not *repeatedly* auto-generated, the way docs might be. They're frozen forever, so can be safely edited after the fact.