add code to clean up empty data and hintfiles

This fix is meant to fix #136. I am concerned about the potential for this to delete something in error, but I am not sure how best to test it/trigger it.  I can't think of anything that would cause this to delete accessible data, but that doesn't mean there isn't a way.

There is another potential fix that doesn't involve deletion, but that will only work in 2.0 after #128 lands.

@slfritchie @engelsanchez if you could take a look, this is considered a blocker for 1.4.8.