Change bullets in affiliated package instructions to numbers

While this looks like a lot, this is actually quite simple - it just changes the steps in the affiliated package instructions to be numbered instead of bulleted.  I think it's a lot easier with long lists like this to keep track of where you are.  (Note that the ``#.`` is automatically converted to an actual number by sphinx/ReST).

@astrofrog @cdeil - any objections to this?