Some tweaks based on real usage

The first two commits are trivial - just some cleanups and usability things.  The 3rd commit is a little more involved.

I was incorrectly handling the digests file when re-digesting just a set of paths (as opposed to everything).  It would removal all digests except the set you were digesting.  It has been updated to just modify the set you are digesting.

@jcredding ready for review.