Fix "read-tree -m A B" priming the cache-tree

Fix "read-tree -m A B" priming the cache-tree

In 456156d a shortcut to priming the index tree reference was
introduced, but the justification for it was completely bogus.

"read-tree -m A B" is to take the index (and the working tree)
that is largely based on (but does not have to match exactly) A
and update it to B, while carrying the local change that does
not overlap the difference between A and B, so there is no reason
to expect that the resulting index should match the tree B.

Noticed and test provided by Heiko Voigt.

Signed-off-by: Junio C Hamano <gitster@pobox.com>