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

Also, fix annotations are 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 multiple setter methods and fix the misleading parameters in SetIJKToRASDirections in vtkMRMLVolumeNode.
Fixes #2980
Fixes #3246
Fixes #3256