Non-recursive checkout creates empty directpries in place of submodules.
If then I try to "checkout --to" submodules there, it refuses to do so,
because directory already exists.
Fix by allowing checking out to empty directory. Add test and modify the
existing one so that it uses non-empty directory.
Signed-off-by: Max Kirillov <max@max630.net> Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com> Signed-off-by: Junio C Hamano <gitster@pobox.com>