Ah, I don't see it because the Python build uses md5. Doesn't cmake?

I don't think 'make' is the annoyance here, at least, not to me. If I recall correctly, last time, Barry couldn't stand emac's insistence on asking 'should I reload this buffer' even when nothing changed on disk except for the timestamp. Following this thread:

http://stackoverflow.com/questions/665600/how-can-i-get-emacs-to-revert-all-unchanged-buffers-when-switching-branches-in-g

you can either set (global-auto-revert-mode) or try using the revbufs extension.