Brings /opt/kubernetes in line with config that was applied directly
on the server: catalogue DB and S3 credentials/config in
nearle-config.yaml and nearle-app-secrets.yaml, and deploy scripts
switched to kubectl apply -k against the kustomize manifests. Also
dedupes USE_S3/S3_ENDPOINT/S3_BUCKET/S3_REGION which were listed
twice in nearle-config.yaml.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>