Copy/Paste is working. Any shape can be copy pasted using Control+C/Control+V. It simply copy the selected shape content to a new entity. I've also made a mini clipboard manager, so at the moment will be possible to select multiple shapes, the clipboard will need minimal changes to be extended to use all those shapes.
The deleted nodes will be removed from tree silently at save. The deleted nodes are considered the hidden nodes (like the ones when you press Delete key) and are not referenced by other shapes.
In the past the Property Grid was dependent for X, Y, Z coordinate members to have an associated Point3D (or vertex). Right now is created one that pack an X, Y, Z value without need to create an child vertex. Transformations property is translated to this new visual descriptor.