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You can have your eks resources in a file `cluster.ts`, and have your `system` + `apps` files import the resources from there.
Your `index.ts` can import everything safely.


It's also worth looking into Component Resources, which use classes that you can initialise with dependencies.
<https://www.pulumi.com/docs/concepts/resources/components/|https://www.pulumi.com/docs/concepts/resources/components/>