I dont know if this is even fixable, but I wanted to at least mention it. Performing a git stash will destroy any hard links and replace them with simply a copy of the file. $ mkdir test $ cd test $ git init $ touch foobar.sh $ git add -A $ git commit -m 'first commit' $ ln foobar.sh foobar-link.sh $ ls -l total 0 -rw-r--r-- 2 Steven None 0 May 21 23:18 foobar.sh -rw-r--r-- 2 Steven None 0 May 21 23:18 foobar-link.sh $ git stash -u $ git stash pop $ ls -l total 0 -rw-r--r-- 1 Steven None 0 May 21 23:18 foobar.sh -rw-r--r-- 1 Steven None 0 May 21 23:18 foobar-link.sh -- 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