BUG: Fix "volume not marked as modified on Save after harden transform".

Also, fix "annotations not marked as modified on save after they are changed". Anytime a vtkMRMLStorableNode property that is saved in file is modified, the StorableModifiedTime time stamp must be modified.
Third, refactor setter methods SetIJKToRASDirections and fix its misleading parameters in vtkMRMLVolumeNode.
Fixes #2980
Fixes #3246
Fixes #3256