I wonder if the methods removeNode and removeRelationship can be made accessible by the zest core. At the moment, they are part of AbstractStructuredGraphViewer. This is not exported and GraphViewer does not override them.
It means that I cannot properly delete nodes from a graph.
I don't think it's really an intended part of the design to be editing the (view) graph nodes and edges directly. A much better approach is to use a backing model and then provide context menu items to remove the node form the backing model. Then on refresh Zest will handle the rest.