Fix automodapi :skip: directive

This addresses #983 (for some reason I couldn't get it to attach to the issue).

This one was pretty straightforward to fix, but surprisingly tricky to track down the root cause... I think :skip: was actually never working at all in ``:automodapi:``.  But this makes it work correctly when I try `:skip:`ing something in the astropy docs.  @astrofrog , can you check it on `aplpy` to make sure it resolves the original issue in #983?

@iguananaut - this should go into v0.2.2 if possible, give that I'm pretty sure this commit fixes it and the feature is completely broken otherwise