clone: prevent --reference to a shallow repository

clone: prevent --reference to a shallow repository

If we borrow objects from another repository, we should also pay
attention to their $GIT_DIR/shallow (and even info/grafts). But
current alternates code does not.

Reject alternate repos that are shallow because we do not do it
right. In future the alternate code may be updated to check
$GIT_DIR/shallow properly so that this restriction could be lifted.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>