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Not really that I know of. For starters "projects" are a Rancher thing - not a k8s one. I mean if you want to run only the components needed to run the cluster you can always rebuild a new cluster without the apps I guess.

I would like to verify the installed system components before the payload is started. Its useless to proceed at startup time if Longhorn has severe problems, the S3 storage cannot be reached, or if some control plane node is still cordoned and forgotten.

Kubernetes in general is definitely designed more towards the 'eventual consistency' pattern. Meaning as opposed to starting applications in stages it prefers starting applications all together and looping until dependencies are finished being created. Could you put your longhorn checks as part of the application 'init container' sidecar maybe? Init containers allow you to run something to completion before starting the main application (https://kubernetes.io/docs/concepts/workloads/pods/init-containers/). I hope this helps!