merge-recursive: Split update_stages_and_entry; only update stages at end

Instead of having the process_renames logic update the stages in the index
for the rename destination, have the index updated after process_entry or
process_df_entry.  This will also allow us to have process_entry determine
whether a file was tracked and existed in the working copy before the
merge started.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>