The right click and delete in the Models module will delete hierarchies nodes associated with model nodes, but the Data module doesn't take this into account. When the tree is in Transform mode, the model hierarchy nodes are hidden, but the Models module shows them.

The vtkMRMLScene has been set up to clean up associated nodes when displayable nodes are deleted, but only storage and display so far I think. Adding a check for a hierarchy node that only points to the node deleted might be prone to errors.

I'm not 100% sure that the Data module should be deleting hierarchy nodes either, especially as they can only been seen when Show Hidden nodes is checked.

Note that I deleted a model node, not a model hierarchy node. Deletion of the model node resulted in the "creation" of a new model hierarchy node (visible in the Model module)

The Models module hierarchy looks fine now after deleting a model in the Data module.

Closing resolved issues that have not been updated in more than 3 months