combine idifference.py and idifference2.py

I don't think that it's useful to have both. Can we combine them?

My intent was to replace idifference with what's in idifference2. I wrote idifference2 for a paper, and then needed to prioritize graduating, so that's why it has hung around a while. As I recall there were a last few flags to re-implement for feature parity.

I think this will be good to revisit as we consider command line tool setup via setup.cfg.