Python/context: python could get invalid bpy.data in scene update handler after

Python/context: python could get invalid bpy.data in scene update handler after
undo.

The way this got updated from the context is a bit unreliable, and for handlers
the update couldn't happen because there is no context passed in. Now it's
updated from setup_app_data, which is where the change actually happens. I left
in the other updates to be sure but they should not be needed anymore.