[eropple]

This is always a tough spot in JSON, I think. You want the `id` in the node or edge object, but you also want uniqueness. I don't think there's a great way to get this any be able to just `JSON.parse()` and go without further fixup.

[Retr0id]

What do you concretely gain from embedding the id within the object?

[Macha]

You have a reference to an object, maybe found by filtering the list based on co-ordinate intersection, and you need its ID to put somewhere else (e.g. in the "to" field of an edge). Sure, all your find/filter methods could return (ID, object) or just return an ID and make you do a second lookup to find the object, but at the kind of object counts we're talking about for this implementation, a small amount of extra memory to have the ID as a field in exchange for a nicer API is a reasonable tradeoff.