The "update-index followed by checkout-index" chain served two
purposes -- to collapse the index to "our" version, and make
sure that file exists in the working tree.  In the recent update
to leave the index unmerged on conflicting path, we wanted to
stop doing the former, but we still need to do the latter (we
allow merging to work in an un-checked-out working tree).

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