When I run ./bootstrap, it creates generates massive diffs (Makefile.in, configure, aclocal.m4, build-aux) as compared to the checked-in versions.

 80 files changed, 19707 insertions(+), 7912 deletions(-)

This makes 'git diff' worthless and I have to 'git checkout .' before 'git pull'. Is your idea that users will never run ./bootstrap? If so, how do you avoid 20kLOC changes every time a different person updates the generated files?