Fix null YAML values being replaced by "null"

Related issues:

* https://github.com/kubernetes-sigs/kustomize/issues/5031
* https://github.com/kubernetes-sigs/kustomize/issues/5171

After noting this behaviour was not present in
d89b448c74 a `git bisect` pointed to the
change 1b7db20504. The issue with that
change is that upon seeing a `null` node it would replace it with a node
whose value was equivalent but without a `!!null` tag. This meant that
one application of a patch would have the desired approach: the result
would be `null` in the output, but on a second application of a similar
patch the field would be rendered as `"null"`.

To avoid this, define a new attribute on `RNode`s that is checked before
clearing any node we should keep. The added
`TestApplySmPatch_Idempotency` test verifies this behaviour.

See also https://github.com/kubernetes-sigs/kustomize/pull/5365 for an
alternative approach

api/resource/resource_test.go

@@ -9,6 +9,7 @@ import (
 	"testing"
 
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
 	"sigs.k8s.io/kustomize/api/internal/utils"
 	"sigs.k8s.io/kustomize/api/provider"
 	. "sigs.k8s.io/kustomize/api/resource"
@@ -281,6 +282,43 @@ spec:
 `, string(bytes))
 }
 
+// regression test for https://github.com/kubernetes-sigs/kustomize/issues/5031
+func TestApplySmPatch_Idempotency(t *testing.T) {
+	// an arbitrary number of times to apply the patch
+	patchApplyCount := 4
+	resourceYaml := `apiVersion: v1
+kind: Deployment
+metadata:
+  creationTimestamp: null
+  labels: null
+  name: my-deployment
+`
+	resource, err := factory.FromBytes([]byte(resourceYaml))
+	require.NoError(t, err)
+
+	noOpPatch, err := factory.FromBytes([]byte(`
+apiVersion: v1
+kind: Deployment
+metadata:
+  name: my-deployment
+`))
+	require.NoError(t, err)
+
+	for i := 0; i < patchApplyCount; i++ {
+		require.NoError(t, resource.ApplySmPatch(noOpPatch))
+
+		bytes, err := resource.AsYAML()
+		require.NoError(t, err)
+
+		require.Equal(
+			t,
+			resourceYaml,
+			string(bytes),
+			"resource should be unchanged after re-application of patch",
+		)
+	}
+}
+
 func TestApplySmPatchShouldOutputListItemsInCorrectOrder(t *testing.T) {
 	cases := []struct {
 		name           string