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

kyaml/yaml/merge2/merge2.go

@@ -66,8 +66,7 @@ func (m Merger) VisitMap(nodes walk.Sources, s *openapi.ResourceSchema) (*yaml.R
 
 		// If Origin is missing, preserve explicitly set null in Dest ("null", "~", etc)
 		if nodes.Origin().IsNil() && !nodes.Dest().IsNil() && len(nodes.Dest().YNode().Value) > 0 {
-			// Return a new node so that it won't have a "!!null" tag and therefore won't be cleared.
-			return yaml.NewScalarRNode(nodes.Dest().YNode().Value), nil
+			return yaml.MakePersistentNullNode(nodes.Dest().YNode().Value), nil
 		}
 
 		return nodes.Origin(), nil

kyaml/yaml/merge2/scalar_test.go

@@ -197,6 +197,22 @@ field: null
 		expected: `
 kind: Deployment
 field: null
+`,
+		mergeOptions: yaml.MergeOptions{
+			ListIncreaseDirection: yaml.MergeOptionsListAppend,
+		},
+	},
+	{description: `keep scalar -- missing in src, null in dest, preserves null marker`,
+		source: `
+kind: Deployment
+`,
+		dest: `
+kind: Deployment
+field: ~
+`,
+		expected: `
+kind: Deployment
+field: ~
 `,
 		mergeOptions: yaml.MergeOptions{
 			ListIncreaseDirection: yaml.MergeOptionsListAppend,