When applying a patch to index file, we need to know where GIT_DIR is;
use setup_git_directory() to find it out.  This also allows us to work
from a subdirectory if we wanted to.

When git-apply is run from a subdirectory, it applies the given patch
only to the files under the current directory and below.

Signed-off-by: Junio C Hamano <junkio@cox.net>