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Is this the only way?

There are many way to do it, this example is a for a simple setup where all apps are applied by a single Flux Kustomization. If you follow this example, then the substitutions must go into clusters/production/apps.yaml for all apps.

Check out the D2 example repos for a complex setup where substitutions are used https://github.com/controlplaneio-fluxcd/d2-fleet

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