When update-trees::threeway_merge() decides that a path that
exists in the current index (and HEAD) is to be removed, it
leaves a stage 0 entry whose mode bits are set to 0.  The code
mistook it as "this stage wants the blob here", and proceeded
to call update_file_flags() which ended up trying to put the
mode=0 entry in the index, got very confused, and ended up
barfing with "do not know what to do with 000000".

Since threeway_merge() does not handle case #10 (one side
removes while the other side does not do anything), this is not
a problem while we refuse to merge branches that have D/F
conflicts, but when we start resolving them, we would need to be
able to remove cache entries, and at that point it starts to
matter.
Signed-off-by: NJunio C Hamano <junkio@cox.net>