apply: fix infinite loop with multiple patches with --index

apply: fix infinite loop with multiple patches with --index

When multiple patches are passed to git-apply, it will attempt
to open multiple file descriptors to an index, which means
multiple entries will be in the circular cache_file_list.

This change makes git-apply only open the index once and
write the index at exit.

Signed-off-by: Eric Wong <normalperson@yhbt.net>
Signed-off-by: Junio C Hamano <junkio@cox.net>