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Some useful methods, such as addNode, removeNode, addRelationship, removeRelationship (and possibly others, unless they're specifically meant to be non-API) should be made API -- declared in a class/interface in an exported package (e.g., re-declared in GraphViewer). Currently they're not visible to the outside world due to package access restrictions on the plugin.
Re-assigning back to inbox, as Ian is no longer active committer.