Program: 62347
Project: 62347
Buggy source:
private void startApp(final Stage stage,final CmdlineConfig config) throws Throwable {
  final FXMLLoader parentLoader=new FXMLLoader();
  final FXMLLoader asciidocTableLoader=new FXMLLoader();
  final FXMLLoader markdownTableLoader=new FXMLLoader();
  context=SpringApplication.run(SpringAppConfig.class);
  asciidocTableLoader.setControllerFactory(context::getBean);
  markdownTableLoader.setControllerFactory(context::getBean);
  parentLoader.setControllerFactory(context::getBean);
  InputStream asciidocTableStream=getClass().getResourceAsStream("String_Node_Str");
  AnchorPane asciidocTableAnchor=asciidocTableLoader.load(asciidocTableStream);
  InputStream markdownTableStream=getClass().getResourceAsStream("String_Node_Str");
  AnchorPane markdownTableAnchor=markdownTableLoader.load(markdownTableStream);
  InputStream sceneStream=getClass().getResourceAsStream("String_Node_Str");
  Parent root=parentLoader.load(sceneStream);
  controller=parentLoader.getController();
  Scene scene=new Scene(root);
  scene.getStylesheets().add("String_Node_Str");
  stage.setMaximized(true);
  stage.setTitle("String_Node_Str");
  InputStream logoStream=getClass().getResourceAsStream("String_Node_Str");
  stage.getIcons().add(new Image(logoStream));
  Stage asciidocTableStage=new Stage();
  asciidocTableStage.setScene(new Scene(asciidocTableAnchor));
  asciidocTableStage.setTitle("String_Node_Str");
  asciidocTableStage.initModality(Modality.WINDOW_MODAL);
  asciidocTableStage.initOwner(scene.getWindow());
  asciidocTableStage.getIcons().add(new Image(logoStream));
  Stage markdownTableStage=new Stage();
  markdownTableStage.setScene(new Scene(markdownTableAnchor));
  markdownTableStage.setTitle("String_Node_Str");
  markdownTableStage.initModality(Modality.WINDOW_MODAL);
  markdownTableStage.initOwner(scene.getWindow());
  markdownTableStage.getIcons().add(new Image(logoStream));
  IOUtils.closeQuietly(asciidocTableStream);
  IOUtils.closeQuietly(markdownTableStream);
  IOUtils.closeQuietly(sceneStream);
  IOUtils.closeQuietly(logoStream);
  controller.setStage(stage);
  controller.setScene(scene);
  controller.setAsciidocTableAnchor(asciidocTableAnchor);
  controller.setMarkdownTableAnchor(markdownTableAnchor);
  controller.setAsciidocTableStage(asciidocTableStage);
  controller.setMarkdownTableStage(markdownTableStage);
  controller.initializeSaveOnBlur();
  stage.setScene(scene);
  stage.show();
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.S,SHORTCUT_DOWN),controller::saveDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.M,SHORTCUT_DOWN),controller::adjustSplitPane);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.N,SHORTCUT_DOWN),controller::newDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.O,SHORTCUT_DOWN),controller::openDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.W,SHORTCUT_DOWN),controller::saveAndCloseCurrentTab);
  final ThreadService threadService=context.getBean(ThreadService.class);
  threadService.start(() -> {
    try {
      registerStartupListener(config);
    }
 catch (    Exception e) {
      logger.error("String_Node_Str",e);
    }
  }
);
  scene.getWindow().setOnCloseRequest(controller::closeAllTabs);
  if (controller.getTabPane().getTabs().isEmpty())   controller.newDoc();
  controller.setHostServices(getHostServices());
}

Fixed version (ground truth):
private void startApp(final Stage stage,final CmdlineConfig config) throws Throwable {
  final FXMLLoader parentLoader=new FXMLLoader();
  final FXMLLoader asciidocTableLoader=new FXMLLoader();
  final FXMLLoader markdownTableLoader=new FXMLLoader();
  context=SpringApplication.run(SpringAppConfig.class);
  asciidocTableLoader.setControllerFactory(context::getBean);
  markdownTableLoader.setControllerFactory(context::getBean);
  parentLoader.setControllerFactory(context::getBean);
  InputStream asciidocTableStream=getClass().getResourceAsStream("String_Node_Str");
  AnchorPane asciidocTableAnchor=asciidocTableLoader.load(asciidocTableStream);
  InputStream markdownTableStream=getClass().getResourceAsStream("String_Node_Str");
  AnchorPane markdownTableAnchor=markdownTableLoader.load(markdownTableStream);
  InputStream sceneStream=getClass().getResourceAsStream("String_Node_Str");
  Parent root=parentLoader.load(sceneStream);
  controller=parentLoader.getController();
  Scene scene=new Scene(root);
  scene.getStylesheets().add("String_Node_Str");
  stage.setMaximized(true);
  stage.setTitle("String_Node_Str");
  InputStream logoStream=getClass().getResourceAsStream("String_Node_Str");
  stage.getIcons().add(new Image(logoStream));
  Stage asciidocTableStage=new Stage();
  asciidocTableStage.setScene(new Scene(asciidocTableAnchor));
  asciidocTableStage.setTitle("String_Node_Str");
  asciidocTableStage.initModality(Modality.WINDOW_MODAL);
  asciidocTableStage.initOwner(scene.getWindow());
  asciidocTableStage.getIcons().add(new Image(logoStream));
  Stage markdownTableStage=new Stage();
  markdownTableStage.setScene(new Scene(markdownTableAnchor));
  markdownTableStage.setTitle("String_Node_Str");
  markdownTableStage.initModality(Modality.WINDOW_MODAL);
  markdownTableStage.initOwner(scene.getWindow());
  markdownTableStage.getIcons().add(new Image(logoStream));
  IOUtils.closeQuietly(asciidocTableStream);
  IOUtils.closeQuietly(markdownTableStream);
  IOUtils.closeQuietly(sceneStream);
  IOUtils.closeQuietly(logoStream);
  controller.setStage(stage);
  controller.setScene(scene);
  controller.setAsciidocTableAnchor(asciidocTableAnchor);
  controller.setMarkdownTableAnchor(markdownTableAnchor);
  controller.setAsciidocTableStage(asciidocTableStage);
  controller.setMarkdownTableStage(markdownTableStage);
  controller.initializeSaveOnBlur();
  stage.setScene(scene);
  stage.show();
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.S,SHORTCUT_DOWN),controller::saveDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.M,SHORTCUT_DOWN),controller::adjustSplitPane);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.N,SHORTCUT_DOWN),controller::newDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.O,SHORTCUT_DOWN),controller::openDoc);
  scene.getAccelerators().put(new KeyCodeCombination(KeyCode.W,SHORTCUT_DOWN),controller::saveAndCloseCurrentTab);
  final ThreadService threadService=context.getBean(ThreadService.class);
  threadService.start(() -> {
    try {
      registerStartupListener(config);
    }
 catch (    Exception e) {
      logger.error("String_Node_Str",e);
    }
  }
);
  scene.getWindow().setOnCloseRequest(controller::closeAllTabs);
  if (controller.getTabPane().getTabs().isEmpty())   controller.newDoc();
  controller.setHostServices(getHostServices());
  stage.widthProperty().addListener(controller::stageWidthChanged);
  stage.heightProperty().addListener(controller::stageWidthChanged);
}