Program: 96420
Project: 96420
Buggy source:
@Override public void start(final Stage s) throws Exception {
  Application.setUserAgentStylesheet(GLASS_BLACK_SMOKE);
  stage=s;
  stage.getIcons().add(new Image(getClass().getResource("String_Node_Str").toExternalForm()));
  projectsMap=new SampleScanner().discoverSamples();
  buildProjectTree(null);
  leftSideContent=new VBox();
  leftSideContent.setAlignment(Pos.TOP_CENTER);
  leftSideContent.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  leftSideContent.setSpacing(3);
  leftSideContent.setPadding(new Insets(3));
  leftSideContent.getStyleClass().add("String_Node_Str");
  rightSideContent=new VBox();
  rightSideContent.getStyleClass().add("String_Node_Str");
  centerContent=new StackPane();
  centerContent.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  searchBar=new TextField();
  searchBar.setPrefSize(USE_COMPUTED_SIZE,USE_PREF_SIZE);
  searchBar.textProperty().addListener((  Observable o) -> {
    buildProjectTree(searchBar.getText());
  }
);
  contentTree=new TreeView<>(root);
  contentTree.getStyleClass().add("String_Node_Str");
  contentTree.setShowRoot(false);
  contentTree.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  contentTree.setCellFactory(new Callback<TreeView<FXyzSample>,TreeCell<FXyzSample>>(){
    @Override public TreeCell<FXyzSample> call(    TreeView<FXyzSample> param){
      return new TreeCell<FXyzSample>(){
        @Override protected void updateItem(        FXyzSample item,        boolean empty){
          super.updateItem(item,empty);
          if (empty) {
            setText("String_Node_Str");
          }
 else {
            setText(item.getSampleName());
          }
        }
      }
;
    }
  }
);
  contentTree.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TreeItem<FXyzSample>>(){
    @Override public void changed(    ObservableValue<? extends TreeItem<FXyzSample>> observable,    TreeItem<FXyzSample> oldValue,    TreeItem<FXyzSample> newSample){
      if (newSample == null) {
        return;
      }
 else       if (newSample.getValue() instanceof EmptySample) {
        FXyzSample selectedSample=newSample.getValue();
        Project selectedProject=projectsMap.get(selectedSample.getSampleName());
        System.out.println(selectedProject);
        if (selectedProject != null) {
          changeToWelcomePage(selectedProject.getWelcomePage());
        }
        return;
      }
      selectedSample=newSample.getValue();
      changeContent();
    }
  }
);
  leftSideContent.getChildren().addAll(searchBar,contentTree);
  VBox.setVgrow(contentTree,Priority.ALWAYS);
  client=new HiddenSidesClient();
  client.setContent(centerContent);
  client.setLeft(leftSideContent);
  client.setRight(rightSideContent);
  client.setTriggerDistance(15);
  frame=new SimpleWindowFrame(stage,1280,800);
  frame.setIconImage(new Image(getClass().getResource("String_Node_Str").toExternalForm()));
  frame.setText("String_Node_Str");
  frame.setRootContent(client);
  frame.getPinRelease().setOnMouseEntered(e -> {
    if (client.getPinnedSide() != null) {
      client.setPinnedSide(null);
      frame.getPinRelease().toBack();
    }
  }
);
  List<TreeItem<FXyzSample>> projects=contentTree.getRoot().getChildren();
  if (!projects.isEmpty()) {
    TreeItem<FXyzSample> firstProject=projects.get(0);
    contentTree.getSelectionModel().select(firstProject);
  }
 else {
    changeToWelcomePage(null);
  }
  Scene scene=new Scene(frame,1280,800);
  scene.setFill(Color.TRANSPARENT);
  this.stage.setScene(scene);
  this.stage.initStyle(StageStyle.TRANSPARENT);
  this.stage.show();
  System.err.println(contentTree.getRoot().getChildren());
}

Fixed version (ground truth):
@Override public void start(final Stage s) throws Exception {
  Application.setUserAgentStylesheet(GLASS_BLACK_SMOKE);
  stage=s;
  stage.getIcons().add(new Image(getClass().getResource("String_Node_Str").toExternalForm()));
  projectsMap=new SampleScanner().discoverSamples();
  buildProjectTree(null);
  leftSideContent=new VBox();
  leftSideContent.setAlignment(Pos.TOP_CENTER);
  leftSideContent.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  leftSideContent.setSpacing(3);
  leftSideContent.setPadding(new Insets(3));
  leftSideContent.getStyleClass().add("String_Node_Str");
  contentControls=new VBox();
  contentControls.getStyleClass().add("String_Node_Str");
  contentControls.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  centerContent=new StackPane();
  centerContent.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  searchBar=new TextField();
  searchBar.setFocusTraversable(false);
  searchBar.setPrefSize(USE_COMPUTED_SIZE,USE_PREF_SIZE);
  searchBar.textProperty().addListener((  Observable o) -> {
    buildProjectTree(searchBar.getText());
  }
);
  searchBar.setOnMouseEntered(e -> {
    if (client.getPinnedSide() == null) {
      client.setPinnedSide(Side.LEFT);
    }
  }
);
  searchBar.setOnAction(a -> {
    client.setPinnedSide(null);
  }
);
  contentTree=new TreeView<>(root);
  contentTree.getStyleClass().add("String_Node_Str");
  contentTree.setShowRoot(false);
  contentTree.setPrefSize(USE_COMPUTED_SIZE,USE_COMPUTED_SIZE);
  contentTree.setCellFactory(new Callback<TreeView<FXyzSample>,TreeCell<FXyzSample>>(){
    @Override public TreeCell<FXyzSample> call(    TreeView<FXyzSample> param){
      return new TreeCell<FXyzSample>(){
        @Override protected void updateItem(        FXyzSample item,        boolean empty){
          super.updateItem(item,empty);
          if (empty) {
            setText("String_Node_Str");
          }
 else {
            setText(item.getSampleName());
          }
        }
      }
;
    }
  }
);
  contentTree.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TreeItem<FXyzSample>>(){
    @Override public void changed(    ObservableValue<? extends TreeItem<FXyzSample>> observable,    TreeItem<FXyzSample> oldValue,    TreeItem<FXyzSample> newSample){
      if (newSample == null) {
        return;
      }
 else       if (newSample.getValue() instanceof EmptySample) {
        FXyzSample selectedSample=newSample.getValue();
        Project selectedProject=projectsMap.get(selectedSample.getSampleName());
        System.out.println(selectedProject);
        if (selectedProject != null) {
          changeToWelcomePage(selectedProject.getWelcomePage());
        }
        return;
      }
      selectedSample=newSample.getValue();
      changeContent();
    }
  }
);
  contentTree.setFocusTraversable(false);
  leftSideContent.getChildren().addAll(searchBar,contentTree);
  VBox.setVgrow(contentTree,Priority.ALWAYS);
  client=new HiddenSidesClient();
  client.setContent(centerContent);
  client.setLeft(leftSideContent);
  client.setTriggerDistance(20);
  frame=new SimpleWindowFrame(stage,1280,800);
  frame.setIconImage(new Image(getClass().getResource("String_Node_Str").toExternalForm()));
  frame.setText("String_Node_Str");
  frame.setRootContent(client);
  List<TreeItem<FXyzSample>> projects=contentTree.getRoot().getChildren();
  if (!projects.isEmpty()) {
    TreeItem<FXyzSample> firstProject=projects.get(0);
    contentTree.getSelectionModel().select(firstProject);
  }
 else {
    changeToWelcomePage(null);
  }
  Scene scene=new Scene(frame,1200,768);
  scene.setFill(Color.TRANSPARENT);
  this.stage.setScene(scene);
  this.stage.initStyle(StageStyle.TRANSPARENT);
  this.stage.show();
  System.err.println(contentTree.getRoot().getChildren());
}