Handle multiple preferred-versions in the index tarball better

The existing code supports reading multiple preferred-versions files in
the 00-index.tar and merging them. However it doesn't do it quite right
when the same file is updated, it merged them instead of the later one
overriding the first.

This should make no difference right now because the 00-index.tar
typically only contains a single preferred-versions file, with no
updates.