updated to fix #17

For some reason I can't currently get this to generate rst for the ``qcli/scripts`` directory, but it does work for QIIME. There is some sort of import issue when trying to add ``qcli/scripts`` to ``PYTHONPATH`` with ``addsitedir``. I'm not going to worry about this for now, as this code is going to be completely re-written, and all of the formatting is going to take place in the ``QcliCommand`` class. At that point, this code won't need to modify ``PYTHONPATH``, which will be a much better situation anyway.