js: fix runtime cleanup

This is a minefield.

Intuitively, you would think that just clearing the opaque and manually
freeing registered object should be enough. Unfortunately, this is
not true; we do not store whether we are actually holding a reference to
registered JS objects, so this approach leads to double frees.

Instead, we add a QJS callback that is called right after the final
GC cleanup, but before the list_free assertion. This way, we can be sure
that any object still in our registry is referenced by us, and can
therefore unreference them safely.

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