Update existing transpiler passes to support final_permutation

[jakelishman]

Depending on the results of the conversation here: #9523 (comment), there are a few transpiler passes that would also need updating to support either final_layout (the current form) or final_permutation (a proposed alternate form).

Needed in all cases

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1. OptimizeSwapBeforeMeasure

Needed if we replace final_layout

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1. ApplyLayout
2. EnlargeWithAncilla
3. SabreLayout
4. BasicSwap
5. LookaheadSwap
6. SabreSwap
7. StochasticSwap

I think it's a current bug in O3 that OptimizeSwapBeforeMeasure can modify the virtual mapping at the end of the circuit without updating the final layout in a way that the routers will detect. Using the explicit permutation form as part of the IR (in both virtual and physical domains) as we were talking about in #9523 (comment) would be a good way of avoiding that happening.