union merge bugfix

Union merges involving two or more repositories could sometimes result in
data from one repository getting lost. This could result in the location
log data becoming wrong, and fsck being needed to fix it.

NB: I audited for any other occurrences of this problem. There are other
places than union merge where multiple changes are fed into update-index
in a stream, but they all involve working copy files being staged, or their
deletion being staged, and in this case it's fine for the later changes
to override the earlier ones.

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