Cleanup

This includes the code from pull request https://github.com/OpenTreeOfLife/peyotl/pull/22 I'm not sure if that is bad form...

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.