This swaps the whole Sabre algorithm over to using physical qubits
rather than virtual qubits.  This makes all operations based on finding
the swaps and scoring them far more natural, at the cost of the layer
structures needing to do a little more book-keeping to rewrite
themselves in terms of the new physical qubits after a swap.  This also
means that the swaps that come out of the Sabre algorithm automatically
become physical, which requires less tracking to output them into the
final DAG circuit.

The test outputs change slightly because the order we filter out
duplicate swaps in `obtain_swaps` is not identical.  We filter out cases
where the left index is greater than the right, and with the assignments
of virtual qubits to physical qubits varying, doing the filter with
physical indices in not guaranteed to filter in the same order as doing
it with virtual indices (though the trialled swaps will be the same).

On modern hardware, branching is typically more expensive than a simple
floating-point addition that can be pipelined in.  This removes the
branch in favour of removing the duplication from the scoring at the end
by dividing by two.