Unity SaveHook to save all persistencyIds

SaveHook

using UnityEngine;
using UnityEditor;
using JSONPersistency;
using UnityEditor.Callbacks;

public class SaveSceneHook : AssetModificationProcessor
{
	static string[] OnWillSaveAssets (string[] paths)
	{

		Object[] objs = Component.FindObjectsOfType (typeof(JSONPersistent));

		//Debug.Log ("OnWillSaveAssets " + objs.Length);

		foreach (Object obj in objs) {
			JSONPersistent persist = (JSONPersistent)obj;
			if (!persist.persistentIDisSet ()) {
				persist.loadPersistentID ();
				//Debug.Log (persist.name + " loaded!  persistID: " + persist.getPersistentID ());

			} else {
				//Debug.Log (persist.name + " persistID: " + persist.getPersistentID ());
			}
		}

		return paths;
	}
} 

this is not work with prefabs in Unity5, because the value LocalIdentfierInFile is 0.

Correct, in Unity 5 that doesn't same to work anymore. More here:
https://forum.unity3d.com/threads/how-to-get-the-local-identifier-in-file-for-scene-objects.265686/#post-1901969