BUG: 3241 Fix transform not applied to volume when scene is read from a file

When a scene is loaded, vtkMRMLScene::UpdateNodeReferences doesn't handle event registration.
Except for vtkCommand::ModifiedEvent, any other events need to be registered via OnNodeReferenceAdded API.
Fixes #3241

From: Yuzheng Zhou <yuzheng.zhou@kitware.com>

git-svn-id: http://svn.slicer.org/Slicer4/trunk@22343 3bd1e089-480b-0410-8dfb-8563597acbee
BUG: remove color table entries from mrml file

Rely on the file written to disk by the storage node, 
reduces the size of the mrml file.
Keep the number of colors in the mrml file so that the
table is properly initialised.

Issue #2486


git-svn-id: http://svn.slicer.org/Slicer4/trunk@22344 3bd1e089-480b-0410-8dfb-8563597acbee