Program: 56766
Project: 56766
Buggy source:
@Override public void display(GL2 gl){
  clearWindowStubSets();
  if (windowToSetActive != null) {
    windowToSetActive.setActive(true);
    windowToSetActive=null;
  }
  boolean updateAugmentation=false;
  if (isLayoutDirty)   updateAugmentation=true;
  final boolean isPickingRun=GLGraphics.isPickingPass(gl);
  if (!isPickingRun) {
    if (!contextMenuItemsToShow.isEmpty()) {
      for (      AContextMenuItem item : contextMenuItemsToShow) {
        getContextMenuCreator().add(item);
      }
      contextMenuItemsToShow.clear();
    }
  }
  super.display(gl);
  if (wasContextChanged) {
    vertexSelectionManager.removeFromType(SelectionType.SELECTION,currentContextVertexRep.getID());
    vertexSelectionManager.addToType(SelectionType.SELECTION,currentContextVertexRep.getID());
    vertexSelectionManager.triggerSelectionUpdateEvent();
  }
  if (wasPathwayAdded) {
    EnablePathSelectionEvent event=new EnablePathSelectionEvent(isPathSelectionMode);
    event.setEventSpace(pathEventSpace);
    eventPublisher.triggerEvent(event);
    if (currentContextVertexRep != null) {
      ShowNodeContextEvent e=new ShowNodeContextEvent(currentContextVertexRep);
      e.setEventSpace(pathEventSpace);
      e.setSender(this);
      eventPublisher.triggerEvent(e);
    }
    PathwayMappingEvent pathwayMappingEvent=new PathwayMappingEvent(dataMappingState.getPathwayMappedTablePerspective());
    event.setEventSpace(pathEventSpace);
    EventPublisher.trigger(pathwayMappingEvent);
    EventPublisher.trigger(new SampleMappingModeEvent(sampleMappingMode));
    wasPathwayAdded=false;
  }
  if (updateAugmentation) {
    updateAugmentation();
  }
  dndController.handleDragging(gl,glMouseListener);
}

Fixed version (ground truth):
@Override public void display(GL2 gl){
  clearWindowStubSets();
  if (windowToSetActive != null) {
    windowToSetActive.setActive(true);
    windowToSetActive=null;
  }
  boolean updateAugmentation=false;
  if (isLayoutDirty)   updateAugmentation=true;
  final boolean isPickingRun=GLGraphics.isPickingPass(gl);
  if (!isPickingRun) {
    if (!contextMenuItemsToShow.isEmpty()) {
      for (      AContextMenuItem item : contextMenuItemsToShow) {
        getContextMenuCreator().add(item);
      }
      contextMenuItemsToShow.clear();
    }
  }
  super.display(gl);
  if (wasContextChanged) {
    vertexSelectionManager.removeFromType(SelectionType.SELECTION,currentContextVertexRep.getID());
    vertexSelectionManager.addToType(SelectionType.SELECTION,currentContextVertexRep.getID());
    vertexSelectionManager.triggerSelectionUpdateEvent();
  }
  if (wasPathwayAdded) {
    EnablePathSelectionEvent event=new EnablePathSelectionEvent(isPathSelectionMode);
    event.setEventSpace(pathEventSpace);
    eventPublisher.triggerEvent(event);
    PathwayMappingEvent pathwayMappingEvent=new PathwayMappingEvent(dataMappingState.getPathwayMappedTablePerspective());
    event.setEventSpace(pathEventSpace);
    EventPublisher.trigger(pathwayMappingEvent);
    EventPublisher.trigger(new SampleMappingModeEvent(sampleMappingMode));
    if (currentContextVertexRep != null) {
      ShowNodeContextEvent e=new ShowNodeContextEvent(currentContextVertexRep);
      e.setEventSpace(pathEventSpace);
      e.setSender(this);
      eventPublisher.triggerEvent(e);
    }
    wasPathwayAdded=false;
  }
  if (updateAugmentation) {
    updateAugmentation();
  }
  dndController.handleDragging(gl,glMouseListener);
}