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The original clone logic was causing issue because it clones Set into empty objects, but since scopeIds is the only thing and it doesn't need to be cloned, the simpler fix is to make sure the object clone logic only applies to real plain objects (a4bcbe8). Set and Map can be reused as-is assuming they are immutable on the ASTs.

Also, there are faster ways to clone Sets and Maps, because both are iterable and both accept interables as the constructor argument:

const clonedSet = new Set(originalSet)
const clonedMap = new Map(originalMap)