Remove/reword existing references to 2to3

Just trying to make documentation clear that 2to3 is no longer used in `astropy`. This is therefore a continuation of #2033.

I also removed the `test_run_after_2to3` test in this PR, and enabled the path fixing for coverage tests for python3.
It's a good point about affiliated packages. I actually like the PY3 output better anyways, and think it's not clear that the PY3 output isn't a source path either. I'll restore the previous behavior.