CleanUp#clean: Replace `#destroy_*` calls with `#run_methods`

It turns out that we don't care about destroying orphaned data. From
Alban:

> Quand on duplique un JDD, on lance un CleanUp, sauf que la partie
> "suppression des données orphelines" n'intéresse personne au final.

Replace the calls to
`#destory_{vehicle_journeys,journey_patterns,routes}` with one to
`#run_methods`. This change allows callers to run any cleanup methods
defined in `CleanUp`. For example:

    CleanUp.new(methods: [:destory_routes])

But now by default, none of these destroy methods are run, saving us
from doing extra work that it turns out we don't need to bother doing.

Refs #6854

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