Reference godot class when putting godot scenes in the manifest

[yankscally]

Sometimes a scene may use a class at the root that is not included with the manifest.

We need to do one of these things:

• "The class for the root is not in the manifest" where the menu usually is

• automatically add the class and add the controls for it (not my favourite)

• add the class into the manifest for that scene in the JSON file

• most optimal way, have a flat array of all classes, and reference the index.