prune: check SEEN flag for reachability

The git-prune command checks reachability by doing a traversal, and then
checking whether a given object exists in the global object hash. This
can yield false positives if any other part of the code had to create an
object struct for some reason. It's not clear whether this is even
possible, but it's more robust to rely on something a little more
concrete: the SEEN flag set by our traversal.

Note that there is a slight possibility of regression here, as we're
relying on mark_reachable_objects() to consistently set the flag.
However, it has always done so, and we're already relying on that fact
in prune_shallow(), which is called as part of git-prune. So this is
making these two parts of the prune operation more consistent.

Signed-off-by: Jeff King <peff@peff.net>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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