I think there's a bug in git pull. Doing a git pull in a fresh repository without any commits removes files in the index. Example: $ mkdir foo $ cd foo $ git init $ touch file1 file2 $ git add file1 $ ls file1 file2 $ git pull https://github.com/sos4nt/empty.git master $ ls file2 "file2" is still there, but "file1" was silently removed and no error message was shown. I'm running git 1.8.3.1 Cheers, Stefan-- To unsubscribe from this list: send the line "unsubscribe git" in the body of a message to majordomo@xxxxxxxxxxxxxxx More majordomo info at http://vger.kernel.org/majordomo-info.html