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They dependencies are mostly built based on the Input/Output values (Every Output<T> tracks the resource that created it), but you can also set explicit dependencies via the dependsOn resource option.

Ah, so it's tracking the dependencies between resources, rather than between stacks.

yes

By default, I believe all resources unless they have their parent set are children of a stack resource. If you create a component, add resources to it and assign their parent to the ComponentResource, it changes the graph.