autogen.sh makes git directory dirty

[TheModMaker]

Since there are checked in files generated by autoreconf, running autogen.sh causes the working directory to be dirty with both changed files and untracked files. This is especially annoying since you can't have autoreconf generate files in a different directory to keep the source directory clean.

I notice there is #159, which would probably fix this; but there hasn't been any movement on it in over a year. Would it be possible to merge that PR? Alternatively I could create a PR that just fixes the dirty working directory if that PR is too invasive.