I'll take care of setting the modified flag.

I've noticed this with other CLI code too - I think the issue is that the output of the module is read from a temp directory and thus it is considered 'unmodified' when it really is a new piece of data. I think the CommandLineModuleLogic should be setting the ModifiedSinceRead flag.

A possible complication is that the CommandLineModule only /requests/ the read, which is actually done by the ApplicationLogic so there may be some extra state that needs to get passed.

Fixed in svn 12862.
(side note: the name of this CLI causes the Create New Volume volumes to be named "Resample Scalar/Vector/DWI Volume Volume", and when that's passed into the save data widget, the file name that's created from the node name is just DWI Volume Volume.nrrd because the slashes are read to be directory separators.)