'unpep8' script, which does most of the work.

- topo.py is still in pep8
- not all examples work, but this is due to other issues

It's possible that mn_clean is a bit easier to read; mnclean may be easier
to type, however.

Added variables to Makefile so that source files are listed in a single
location.

This required a change to logging, which now uses a singleton pattern.

For all future checkins, 'make codecheck' should pass.