When running `kubectl rollout restart deployment`, Kubernetes adds the
`kubectl.kubernetes.io/restartedAt` annotation to the deployment's pod
template to trigger a rolling restart. However, Knative's reconciler was
removing this annotation by completely replacing the deployment spec,
causing new pods to be immediately terminated instead of completing the
rollout.

This change preserves externally-added metadata at both the deployment
level and template level during reconciliation by filtering Knative-controlled
keys (*.knative.dev and app label) from the current state before merging with
the desired state. This ensures Knative maintains full control over its own
metadata while preserving external additions.