modified Workflow constructor to add topLevel information

src/main/java/plugins/adufour/protocols/Protocols.java

@@ -362,7 +362,7 @@ public class Protocols extends PluginActionable
             throw new IllegalArgumentException(protocolFile + " is not a valid protocol file");
 
         System.out.println("Loading workflow...");
-        WorkFlow workFlow = new WorkFlow();
+        WorkFlow workFlow = new WorkFlow(true);
         BlocksML.getInstance().loadWorkFlow(xml, workFlow);
 
         workFlow.run();

src/main/java/plugins/adufour/protocols/gui/ProtocolPanel.java

@@ -80,7 +80,7 @@ public class ProtocolPanel extends JPanel implements WorkFlowListener, PropertyC
     
     public ProtocolPanel(MainFrame frame)
     {
-        this(null, new WorkFlow(), frame);
+        this(null, new WorkFlow(true), frame);
     }
     
     private ProtocolPanel(File file, final WorkFlow workFlow, MainFrame frame)