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Forking the discussion from #2433 (comment)
For usage in applications, there's https://secrets-store-csi-driver.sigs.k8s.io/.
For cases where we do need to copy into Kubernetes Secrets, I'd recommend using a similar approach as GitOps, which is copying from the storage system, the secret manager in this case rather than git. In the GitOps layer that could be a special kind of sync request. In the kpt CLI we'll need to figure out how we want to stage secrets before the apply, and ensure we don't leak them.
There's also the issue of generation, for cases where users do want to pre-generate secrets and push them along with their other configuration.