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/fns.go

@@ -724,8 +724,14 @@ func (s FieldSetter) Filter(rn *RNode) (*RNode, error) {
 		return rn, nil
 	}
 
-	// Clear the field if it is empty, or explicitly null
-	if s.Value == nil || s.Value.IsTaggedNull() {
+	// Clearing nil fields:
+	//   1. Clear any fields with no value
+	//   2. Clear any "null" YAML fields unless we explicitly want to keep them
+	// This is to balance
+	//   1. Persisting 'null' values passed by the user (see issue #4628)
+	//   2. Avoiding producing noisy documents that add any field defaulting to
+	//   'nil' even if they weren't present in the source document
+	if s.Value == nil || (s.Value.IsTaggedNull() && !s.Value.ShouldKeep) {
 		return rn.Pipe(Clear(s.Name))
 	}