Make git-clone --use-separate-remote the default

Make git-clone --use-separate-remote the default

We've talked about this for quite some time on the list, and it
is a sane thing to do for a repository with an associcated
working tree.

For somebody who wants to use the traditional layout, there is a
backward compatibility option --use-immingled-remote, but it is
expected to be removed before the next major release.

Signed-off-by: Petr Baudis <redacted>
Signed-off-by: Junio C Hamano <redacted>