Program: 11250
Project: 11250
Buggy source:
@Override public void start(Stage aStage) throws Exception {
  Notifier theNotifier=new Notifier();
  stage=aStage;
  searchPreferences=new SearchPreferences();
  backend=new Backend(theNotifier);
  try {
    searchPreferences.initialize(backend);
    embeddedWebServer=new FrontendEmbeddedWebServer(aStage,backend);
    embeddedWebServer.start();
  }
 catch (  BindException|LockReleaseFailedException e) {
    URL theURL=new URL(FrontendEmbeddedWebServer.getBringToFrontUrl());
    Object theContent=theURL.getContent();
    System.exit(0);
  }
  aStage.setTitle("String_Node_Str");
  aStage.setWidth(800);
  aStage.setHeight(600);
  aStage.initStyle(StageStyle.TRANSPARENT);
  FXMLLoader theLoader=new FXMLLoader(getClass().getResource("String_Node_Str"));
  AnchorPane theMainScene=theLoader.load();
  final DesktopSearchController theController=theLoader.getController();
  theController.configure(this,backend,FrontendEmbeddedWebServer.getSearchUrl(),stage.getOwner());
  Undecorator theUndecorator=new Undecorator(stage,theMainScene);
  theUndecorator.getStylesheets().add("String_Node_Str");
  Scene theScene=new Scene(theUndecorator);
  theUndecorator.setStyle("String_Node_Str");
  theScene.setFill(Color.TRANSPARENT);
  aStage.setScene(theScene);
  aStage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  if (SystemTray.isSupported()) {
    Platform.setImplicitExit(false);
    SystemTray theTray=SystemTray.getSystemTray();
    PopupMenu theMenu=new PopupMenu();
    MenuItem theCloseItem=new MenuItem("String_Node_Str");
    theCloseItem.addActionListener(e -> Platform.runLater(this::shutdown));
    theMenu.add(theCloseItem);
    MenuItem theShowItem=new MenuItem("String_Node_Str");
    theShowItem.addActionListener(e -> Platform.runLater(() -> {
      stage.show();
      stage.toFront();
    }
));
    theMenu.add(theShowItem);
    java.awt.Image theSystrayIcon=Toolkit.getDefaultToolkit().getImage(getClass().getResource("String_Node_Str"));
    TrayIcon theTrayIcon=new TrayIcon(theSystrayIcon,"String_Node_Str",theMenu);
    theTray.add(theTrayIcon);
    aStage.setOnCloseRequest(aEvent -> stage.hide());
  }
 else {
    aStage.setOnCloseRequest(aEvent -> shutdown());
  }
  aStage.show();
}

Fixed version (ground truth):
@Override public void start(Stage aStage) throws Exception {
  Notifier theNotifier=new Notifier();
  stage=aStage;
  searchPreferences=new SearchPreferences();
  backend=new Backend(theNotifier);
  try {
    searchPreferences.initialize(backend);
    embeddedWebServer=new FrontendEmbeddedWebServer(aStage,backend);
    embeddedWebServer.start();
  }
 catch (  BindException|LockReleaseFailedException|LockObtainFailedException e) {
    URL theURL=new URL(FrontendEmbeddedWebServer.getBringToFrontUrl());
    Object theContent=theURL.getContent();
    System.exit(0);
  }
  aStage.setTitle("String_Node_Str");
  aStage.setWidth(800);
  aStage.setHeight(600);
  aStage.initStyle(StageStyle.TRANSPARENT);
  FXMLLoader theLoader=new FXMLLoader(getClass().getResource("String_Node_Str"));
  AnchorPane theMainScene=theLoader.load();
  final DesktopSearchController theController=theLoader.getController();
  theController.configure(this,backend,FrontendEmbeddedWebServer.getSearchUrl(),stage.getOwner());
  Undecorator theUndecorator=new Undecorator(stage,theMainScene);
  theUndecorator.getStylesheets().add("String_Node_Str");
  Scene theScene=new Scene(theUndecorator);
  theUndecorator.setStyle("String_Node_Str");
  theScene.setFill(Color.TRANSPARENT);
  aStage.setScene(theScene);
  aStage.getIcons().add(new Image(getClass().getResourceAsStream("String_Node_Str")));
  if (SystemTray.isSupported()) {
    Platform.setImplicitExit(false);
    SystemTray theTray=SystemTray.getSystemTray();
    PopupMenu theMenu=new PopupMenu();
    MenuItem theCloseItem=new MenuItem("String_Node_Str");
    theCloseItem.addActionListener(e -> Platform.runLater(this::shutdown));
    theMenu.add(theCloseItem);
    MenuItem theShowItem=new MenuItem("String_Node_Str");
    theShowItem.addActionListener(e -> Platform.runLater(() -> {
      stage.show();
      stage.toFront();
    }
));
    theMenu.add(theShowItem);
    java.awt.Image theTrayIconImage=Toolkit.getDefaultToolkit().getImage(getClass().getResource("String_Node_Str"));
    int trayIconWidth=new TrayIcon(theTrayIconImage).getSize().width;
    TrayIcon theTrayIcon=new TrayIcon(theTrayIconImage.getScaledInstance(trayIconWidth,-1,java.awt.Image.SCALE_SMOOTH),"String_Node_Str",theMenu);
    theTrayIcon.setImageAutoSize(true);
    theTrayIcon.setToolTip("String_Node_Str");
    theTrayIcon.addMouseListener(new MouseAdapter(){
      @Override public void mouseClicked(      MouseEvent e){
        if (e.getClickCount() == 1) {
          Platform.runLater(() -> {
            stage.show();
            stage.toFront();
          }
);
        }
      }
    }
);
    theTray.add(theTrayIcon);
    aStage.setOnCloseRequest(aEvent -> stage.hide());
  }
 else {
    aStage.setOnCloseRequest(aEvent -> shutdown());
  }
  aStage.setMaximized(true);
  aStage.show();
}