Teach 'git apply' to look at $GIT_DIR/config

Teach 'git apply' to look at $GIT_DIR/config

When neither --index nor --cached was used, git-apply did not
try calling setup_git_directory(), which means it did not look
at configuration files at all.  This fixes it to call the setup
function but still allow the command to be run in a directory
not controlled by git.

The bug probably meant that 'git apply', not moving up to the
toplevel, did not apply properly formatted diffs from the
toplevel when you are inside a subdirectory, even though 'git
apply --index' would.  As a side effect, this patch fixes it as
well.

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