Docs2: update lots of documentation

This includes the changes in the previous pull request too.  Sorry if that is confusing.  I'm fairly new to git and github.  I'll repeat my comment about the first patch in the series:

I created a long epilog for the prune command. This automatically shows up in usage.html via usage/prune.rst.inc.
I wasn't sure what to do about the existing "Description" for prune in usage.rst, which is now a bit redundant. If all of the Descriptions get moved into epilogs, then all of the Descriptions could just be removed. But the epilogs aren't formatted as nicely as the Descriptions...