Cleanup

There is a bug fix that affects probably no client code (if a phyleystem_api wrapper was called without a statement about the desired output, the default formatting object was not being created correctly). I deployed on devapi, but I'm about to deploy another branch for testing.
The new example/oti_wrapper.py, example/taxomachine_wrapper.py, and example/phylesystem-api-wrapper.py can simply be run (w/o args). There are no tests of the bug fix.