Add instances to sites after removing duplicate ids.

Wait until we've had a chance to remove instances with duplicate ids
before adding instances to their corresponding allocation site.

Reuses the existing iteration over instances that was previously used
for updating registered native sizes and moves that after the
reachability computation in preparation for some anticipated future
changes.

Bug: 110447634
Test: m ahat-test
Test: run ahat on the heap dump from the bug and confirm no duplicate
      instances show up in the list of byte[] instances.

Change-Id: Ie8651d26724148501a7534c9600885002627cd19