Before: 91% methods, 86% lines covered
After: 100% methods, 99% lines covered

This should be the only missing line now:

if (log.isTraceEnabled()) {
  log.trace("Pruned actual resource:\n {} \ndesired resource:\n {} ", actualYaml, desiredYaml);
}

I hope you don't mind the re-ordering of the methods, but I find code always very hard to read if the methods are not sorted by their invocation order. The only changes to the production class are:

• Reorder fields and methods.
• Make getDiff(), sortMap() and sortListItems() static.
• Reformat code comments.
• Make keepOnlyManagedFields() package private (to make it directly testable).