Program: 62361
Project: 62361
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();
  HostServicesDelegate hostServices=HostServicesFactory.getInstance(this);
  controller.setHostServices(hostServices);
  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.F4,SHORTCUT_DOWN),controller::showSettings);
  final ThreadService threadService=context.getBean(ThreadService.class);
  final TabService tabService=context.getBean(TabService.class);
  StartupNotification.registerStartupListener(parameters -> {
    threadService.runActionLater(() -> {
      String[] files=parameters.split("String_Node_Str");
      for (      String file : files) {
        file=file.replace("String_Node_Str","String_Node_Str");
        tabService.addTab(Paths.get(file).toAbsolutePath());
      }
    }
);
  }
);
  if (!config.files.isEmpty()) {
    threadService.runActionLater(() -> {
      config.files.stream().forEach(f -> {
        File file=new File(f).getAbsoluteFile();
        if (file.exists()) {
          logger.info("String_Node_Str",file);
          tabService.addTab(file.toPath());
        }
 else {
          logger.error("String_Node_Str",file);
        }
      }
);
    }
);
  }
  scene.getWindow().setOnCloseRequest(controller::closeAllTabs);
}

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();
  HostServicesDelegate hostServices=HostServicesFactory.getInstance(this);
  controller.setHostServices(hostServices);
  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.F4,SHORTCUT_DOWN),controller::showSettings);
  final ThreadService threadService=context.getBean(ThreadService.class);
  final TabService tabService=context.getBean(TabService.class);
  StartupNotification.registerStartupListener(parameters -> {
    threadService.runActionLater(() -> {
      String[] files=parameters.split("String_Node_Str");
      for (      String file : files) {
        file=file.replace("String_Node_Str","String_Node_Str");
        tabService.addTab(Paths.get(file).toAbsolutePath());
      }
    }
);
  }
);
  if (!config.files.isEmpty()) {
    threadService.runActionLater(() -> {
      config.files.stream().forEach(f -> {
        File file=new File(f).getAbsoluteFile();
        if (file.exists()) {
          logger.info("String_Node_Str",file);
          tabService.addTab(file.toPath());
        }
 else {
          logger.error("String_Node_Str",file);
        }
      }
);
    }
);
  }
  scene.getWindow().setOnCloseRequest(controller::closeAllTabs);
  if (controller.getTabPane().getTabs().isEmpty())   controller.newDoc();
}