We need to rewrite the index file when we check out files, even if we
haven't modified the blob info by reading from another tree, so that
we get the stat cache to include the fact that we just modified the
file so it doesn't need to be refreshed.

While we're at it, move everything that needs to be done to check out
some paths from a tree (or the current index) into checkout_paths().
Signed-off-by: NDaniel Barkalow <barkalow@iabervon.org>
Signed-off-by: NJunio C Hamano <gitster@pobox.com>