CleanUp: Add `#destroy_empty`6854-clean-up--destroy-routes-outside-referential

Gives us a single call site to trigger the destruction of vehicle
journeys, journey patterns, and routes without content.

This was previously done directly in the `#clean` method, but since it's
not needed during referential duplication (only during merges), we don't
want to enable it by default. Thus now to activate the same old
functionality, you would create a `CleanUp` like this:

    CleanUp.new(methods: [:destroy_empty])

Refs #6854

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