As I don't use Stack myself, I have to relay this question here (hope the issue tracker is a good place):

@AshleyYakeley and me aren't sure about whether Stack requires those files for build-type-configure packages to be in Git, see also

haskell/time@409d7a0#commitcomment-15084597

However, if Stack requires to violate VCS/Autoconf conventions, then I'd consider this a bug in Stack ;-)