Fix remaining RTD issues

Fixes the two remaining RTD issues I noted in my [previous pull request](https://github.com/biocore/scikit-bio/pull/234):

- GitHub "Fork me" banner now displays
- Doc rebuilds seem to work if `generated/` is removed before the rebuild

It's probably a good idea to monitor the RTD-hosted site before making it the "official" skbio website just in case there are other issues that show up. Probably by the first release we can switch over to RTD fully.