The following code can be added to PipelineLayoutTool to permit automatic installation of additional menu items in the PLT. Additional file dependencies and examples attached.

protected JMenuBar createMenuBar() {
JISTApplicationPluginBuilder builder = new JISTApplicationPluginBuilder();

toggleItems = new ArrayList();
JMenuBar menuBar = new JMenuBar();
JMenuItem menuItem;
JMenu menuFile = new JMenu("File");
menuFile.setMnemonic(KeyEvent.VK_F);
menuBar.add(menuFile);
JMenu menuEdit = new JMenu("Edit");
menuEdit.setMnemonic(KeyEvent.VK_E);
menuBar.add(menuEdit);
JMenu menuAction = new JMenu("Project");
menuAction.setMnemonic(KeyEvent.VK_P);
menuBar.add(menuAction);
menuItem = new JMenuItem("New");
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_N);
menuItem.addActionListener(this);
menuFile.add(menuItem);
menuItem = new JMenuItem("Open");
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_O);
menuItem.addActionListener(this);
menuFile.add(menuItem);
recentFiles = new JMenu("Recent Files");
menuFile.add(recentFiles);
toggleItems.add(menuItem = new JMenuItem("Save"));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_S);
menuItem.addActionListener(this);
menuFile.add(menuItem);
toggleItems.add(menuItem = new JMenuItem("Save As..."));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_S,
ActionEvent.CTRL_MASK | ActionEvent.SHIFT_MASK));
menuItem.setMnemonic(KeyEvent.VK_A);
menuItem.addActionListener(this);
menuFile.add(menuItem);
toggleItems.add(menuItem = new JMenuItem("Close"));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_W,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_C);
menuItem.addActionListener(this);
menuFile.add(menuItem);
toggleItems.add(menuItem = new JMenuItem("Clear Image Registry"));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_R);
menuItem.addActionListener(this);
menuFile.add(menuItem);

JMenu menuFilePlugins = new JMenu("More ...");
menuFile.add(menuFilePlugins);
menuItem = new JMenuItem("Exit");
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_X);
menuItem.addActionListener(this);
menuFile.add(menuItem);
toggleItems.add(menuItem = new JMenuItem("Delete"));
menuItem.addActionListener(this);
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_DELETE, 0));
menuItem.setMnemonic(KeyEvent.VK_D);
menuEdit.add(menuItem);
removeItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Undo"));
menuItem.addActionListener(this);
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Z,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_U);
menuEdit.add(menuItem);
undoItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Redo"));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Y,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_R);
menuItem.addActionListener(this);
menuEdit.add(menuItem);
redoItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Cut"));
menuItem.addActionListener(this);
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_X,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_T);
menuEdit.add(menuItem);
cutItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Copy"));
menuItem.addActionListener(this);
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_C,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_C);
menuEdit.add(menuItem);
copyItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Paste"));
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_V,
ActionEvent.CTRL_MASK));
menuItem.addActionListener(this);
menuEdit.add(menuItem);
pasteItem = menuItem;
toggleItems.add(menuItem = new JMenuItem("Layout Preferences"));
menuItem.addActionListener(this);
menuAction.add(menuItem);
menuItem = new JMenuItem("Global Preferences");
menuItem.addActionListener(this);
menuAction.add(menuItem);
menuItem = new JMenuItem("Rebuild Library");
menuItem.addActionListener(this);
menuAction.add(menuItem);
/*
* menuItem = new JMenuItem("Set Library Directory");
* menuItem.addActionListener(this); menuAction.add(menuItem);
*/
toggleItems.add(menuItem = new JMenuItem("Process Manager"));
menuItem.addActionListener(this);
menuItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M,
ActionEvent.CTRL_MASK));
menuItem.setMnemonic(KeyEvent.VK_M);
menuAction.add(menuItem);

JMenu menuPlugins = new JMenu("Plug-Ins");
menuPlugins.setMnemonic(KeyEvent.VK_G);
menuBar.add(menuPlugins);

JMenu menuHelp = new JMenu("Help");
menuHelp.setMnemonic(KeyEvent.VK_H);
menuBar.add(menuHelp);
toggleItems.add(aboutItem = new JMenuItem("About"));
aboutItem.addActionListener(this);
menuHelp.add(aboutItem);

JMenu menuActionPlugins = new JMenu("More ...");
menuAction.add(menuActionPlugins);

JMenu menuEditPlugins = new JMenu("More ...");
menuEdit.add(menuEditPlugins);

JISTApplicationPluginBuilder.ContextDataGrabber grabber = new JISTApplicationPluginBuilder.ContextDataGrabber() {
public Object getContextData() {
return LayoutPanel.getInstance().getActiveFrame()
.getPipelineLayout();
}
};
//Specify menus where context data should be displayed.
builder.setMenu(ContextType.MENU_PROJECT, menuActionPlugins);
builder.setMenu(ContextType.MENU_PLUGINS, menuPlugins);
builder.setMenu(ContextType.MENU_HELP, menuHelp);
builder.setMenu(ContextType.MENU_FILE, menuFilePlugins);
builder.setMenu(ContextType.MENU_EDIT, menuEditPlugins);
//Specify grabber for pulling context data.
builder.setGrabber(ContextType.MENU_PROJECT, grabber);
builder.setGrabber(ContextType.MENU_PLUGINS, grabber);
builder.setGrabber(ContextType.MENU_HELP, grabber);
builder.setGrabber(ContextType.MENU_FILE, grabber);
builder.setGrabber(ContextType.MENU_EDIT, grabber);
//Thread installation process.
builder.install();

return menuBar;
}

The following changes are needed to createMenuBar() in
process manager to allow for additional menu options:

/**
* Create menubar.
*
* @return the j menu bar
*/
public JMenuBar createMenuBar() {
toggleItems = new ArrayList();
JMenuBar menuBar = new JMenuBar();
JMenu menuFile = new JMenu("File");
menuFile.setMnemonic(KeyEvent.VK_F);
menuBar.add(menuFile);
toggleItems.add(openItem = new
JMenuItem("Open"));
openItem.setMnemonic(KeyEvent.VK_O);

openItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O
,
ActionEvent.CTRL_MASK));
openItem.addActionListener(this);
menuFile.add(openItem);
recentFiles = new JMenu("Recent Files");
menuFile.add(recentFiles);

toggleItems.add(saveAsItem = new
JMenuItem("Save As"));
saveAsItem.setMnemonic(KeyEvent.VK_A);

saveAsItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK
_S,
ActionEvent.CTRL_MASK));
saveAsItem.addActionListener(this);
menuFile.add(saveAsItem);
toggleItems.add(reloadItem = new
JMenuItem("Reload"));
reloadItem.setMnemonic(KeyEvent.VK_C);

reloadItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK
_R,
ActionEvent.CTRL_MASK));
reloadItem.addActionListener(this);
menuFile.add(reloadItem);
toggleItems.add(closeItem = new
JMenuItem("Close"));
closeItem.setMnemonic(KeyEvent.VK_C);

closeItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_
W,
ActionEvent.CTRL_MASK));
closeItem.addActionListener(this);
menuFile.add(closeItem);
toggleItems.add(prefItem = new
JMenuItem("Layout Preferences"));
prefItem.setMnemonic(KeyEvent.VK_P);
prefItem.addActionListener(this);
menuFile.add(prefItem);
toggleItems.add(globalItem = new
JMenuItem("Global Preferences"));
globalItem.addActionListener(this);
menuFile.add(globalItem);
JMenu menuFilePlugins = new JMenu("More
...");
menuFile.add(menuFilePlugins);
toggleItems.add(quitItem = new
JMenuItem("Quit"));
quitItem.setMnemonic(KeyEvent.VK_Q);
quitItem.addActionListener(this);

quitItem.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Q
,
ActionEvent.CTRL_MASK));
quitItem.setMnemonic(KeyEvent.VK_Q);
menuFile.add(quitItem);
JMenu menuAction = new JMenu("Scheduler");
menuAction.setMnemonic(KeyEvent.VK_S);
menuBar.add(menuAction);
toggleItems.add(runAllItem = new
JMenuItem("Start Scheduler"));
runAllItem.addActionListener(this);
menuAction.add(runAllItem);
toggleItems.add(pauseAllItem = new
JMenuItem(
"Finish Queued / Stop
Enqueue"));
pauseAllItem.addActionListener(this);
menuAction.add(pauseAllItem);
toggleItems.add(destItem = new
JMenuItem("Process Destinations"));
destItem.addActionListener(this);
menuAction.add(destItem);
toggleItems.add(stopAllItem = new
JMenuItem("Stop All"));
stopAllItem.addActionListener(this);
menuAction.add(stopAllItem);
toggleItems.add(cleanAllItem = new
JMenuItem("Clean All"));
cleanAllItem.addActionListener(this);
menuAction.add(cleanAllItem);
JMenu menuPlugins = new JMenu("Plug-Ins");
menuPlugins.setMnemonic(KeyEvent.VK_G);
menuBar.add(menuPlugins);
JMenu menuActionHelp = new JMenu("Help");
menuActionHelp.setMnemonic(KeyEvent.VK_H);
menuBar.add(menuActionHelp);
toggleItems.add(aboutItem = new
JMenuItem("About"));
aboutItem.addActionListener(this);
menuActionHelp.add(aboutItem);

JISTApplicationPluginBuilder builder = new
JISTApplicationPluginBuilder();

JISTApplicationPluginBuilder.ContextDataGrabber grabber =
new JISTApplicationPluginBuilder.ContextDataGrabber() {
public Object getContextData() {
return
ProcessManager.getInstance().managerPane.getTableModel().row
s;
}
};
// Specify menus where context data should
be displayed.
builder.setMenu(ContextType.MENU_PLUGINS,
menuPlugins);
builder.setMenu(ContextType.MENU_HELP,
menuActionHelp);
builder.setMenu(ContextType.MENU_FILE,
menuFilePlugins);
// Specify grabber for pulling context data.
builder.setGrabber(ContextType.MENU_PLUGINS,
grabber);
builder.setGrabber(ContextType.MENU_HELP,
grabber);
builder.setGrabber(ContextType.MENU_FILE,
grabber);
// Thread installation process.
builder.install();

closeItem.setEnabled(false);
runAllItem.setEnabled(false);
stopAllItem.setEnabled(false);
cleanAllItem.setEnabled(true);
pauseAllItem.setEnabled(false);
prefItem.setEnabled(false);
saveAsItem.setEnabled(false);
reloadItem.setEnabled(false);
return menuBar;
}