update-index: make D/F conflict error a bit more verbose.

When you remove a directory D that has a tracked file D/F out of the
way to create a file D and try to "git update-index --add D", it used
to say "cannot add" which was not very helpful.  This issues an extra
error message to explain the situation before the final "fatal" message.

Since D/F conflicts are relatively rare event, extra verbosity would
not make things too noisy.

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