Since b57fb80a7d (init, clone: support --separate-git-dir for .git file)
git clone supports the --separate-git-dir option to create the git dir
outside the work tree. But when that option is used, the git dir won't be
deleted in case the clone fails like it would be without this option. This
makes clone lose its atomicity as in case of a failure a partly set up git
dir is left behind. A real world example where this leads to problems is
when "git submodule update" fails to clone a submodule and later calls to
"git submodule update" stumble over the partially set up git dir and try
to revive the submodule from there, which then fails with a not very user
friendly error message.

Fix that by updating the junk_git_dir variable (used to remember if and
what git dir should be removed in case of failure) to the new value given
with the --seperate-git-dir option. Also add a test for this to t5600 (and
while at it fix the former last test to not cd into a directory to test
for its existence but use "test -d" instead).

Reported-by: Manlio Perillo <manlio.perillo@gmail.com>
Signed-off-by: Jens Lehmann <Jens.Lehmann@web.de>
Signed-off-by: Junio C Hamano <gitster@pobox.com>