Fix up hacking ignores a bit.

Add more explicit ignores to tox.ini hacking ignores until
we have a chance to fix up the imports and docstring errors
we've been ignoring.  This should give us everything we had
in the past (ie alphabetical import checks).

Also, update run_tests.sh to call flake8 and not the hacking.py
that is no longer there.

Change-Id: I6c82e958002255fd9f527b06bf0a68d148cc681e
Merge "Fix up hacking ignores a bit."