submodules: fix of regression on fetching of non-init subsub-repo

submodules: fix of regression on fetching of non-init subsub-repo

A regression has been introduced by a62387b (submodule.c: fetch in
submodules git directory instead of in worktree, 2018-11-28).

The scenario in which it triggers is when one has a remote repository
with a subrepository inside a subrepository like this:
superproject/middle_repo/inner_repo

Person A and B have both a clone of it, while Person B is not working
with the inner_repo and thus does not have it initialized in his working
copy.

Now person A introduces a change to the inner_repo and propagates it
through the middle_repo and the superproject.

Once person A pushed the changes and person B wants to fetch them using
"git fetch" on superproject level, B's git call will return with error
saying:

Could not access submodule 'inner_repo'
Errors during submodule fetch:
         middle_repo

Expectation is that in this case the inner submodule will be recognized
as uninitialized subrepository and skipped by the git fetch command.

This used to work correctly before 'a62387b (submodule.c: fetch in
submodules git directory instead of in worktree, 2018-11-28)'.

Starting with a62387b the code wants to evaluate "is_empty_dir()" inside
.git/modules for a directory only existing in the worktree, delivering
then of course wrong return value.

This patch reverts the changes of a62387b and introduces a regression
test.

Signed-off-by: Peter Kaestle <peter.kaestle@nokia.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>