@Override
  public void addPackagesToChildren(final @NotNull ArrayList<? super AbstractTreeNode<?>> children,
                                    final @Nullable Module module,
                                    final @NotNull TodoTreeBuilder builder) {
    Project project = getProject();
    final PsiManager psiManager = PsiManager.getInstance(project);
    final List<VirtualFile> sourceRoots = new ArrayList<>();
    if (module == null) {
      final ProjectRootManager projectRootManager = ProjectRootManager.getInstance(project);
      ContainerUtil.addAll(sourceRoots, projectRootManager.getContentSourceRoots());
    }
    else {
      ModuleRootManager moduleRootManager = ModuleRootManager.getInstance(module);
      ContainerUtil.addAll(sourceRoots, moduleRootManager.getSourceRoots());
    }
    final Set<PsiPackage> topLevelPackages = new HashSet<>();
    for (final VirtualFile root : sourceRoots) {
      final PsiDirectory directory = psiManager.findDirectory(root);
      if (directory == null) {
        continue;
      }
      final PsiPackage directoryPackage = JavaDirectoryService.getInstance().getPackage(directory);
      if (directoryPackage == null || PackageUtil.isPackageDefault(directoryPackage)) {
        // add subpackages
        final PsiDirectory[] subdirectories = directory.getSubdirectories();
        for (PsiDirectory subdirectory : subdirectories) {
          final PsiPackage aPackage = JavaDirectoryService.getInstance().getPackage(subdirectory);
          if (aPackage != null && !PackageUtil.isPackageDefault(aPackage)) {
            topLevelPackages.add(aPackage);
          } else {
            final Iterator<PsiFile> files = builder.getFiles(subdirectory);
            if (!files.hasNext()) continue;
            TodoDirNode dirNode = new TodoDirNode(project, subdirectory, builder);
            if (!children.contains(dirNode)){
              children.add(dirNode);
            }
          }
        }
        // add non-dir items
        final Iterator<PsiFile> filesUnderDirectory = builder.getFilesUnderDirectory(directory);
        while (filesUnderDirectory.hasNext()) {
          final PsiFile file = filesUnderDirectory.next();
          TodoFileNode todoFileNode = new TodoFileNode(project, file, builder, false);
          if (!children.contains(todoFileNode)){
            children.add(todoFileNode);
          }
        }
      }
      else {
        // this is the case when a source root has pakage prefix assigned
        topLevelPackages.add(directoryPackage);
      }
    }

    GlobalSearchScope scope = module != null ? GlobalSearchScope.moduleScope(module) : GlobalSearchScope.projectScope(project);
    ArrayList<PsiPackage> packages = new ArrayList<>();
    for (PsiPackage psiPackage : topLevelPackages) {
      final PsiPackage aPackage = findNonEmptyPackage(psiPackage, module, project, builder, scope);
      if (aPackage != null){
        packages.add(aPackage);
      }
    }
    for (PsiPackage psiPackage : packages) {
      if (!builder.getTodoTreeStructure().getIsFlattenPackages()) {
        PackageElement element = new PackageElement(module, psiPackage, false);
        TodoPackageNode packageNode = new TodoPackageNode(project, element, builder, psiPackage.getQualifiedName());
        if (!children.contains(packageNode)) {
          children.add(packageNode);
        }
      } else {
        Set<PsiPackage> allPackages = new HashSet<>();
        traverseSubPackages(psiPackage, module, builder, project, allPackages);
        for (PsiPackage aPackage : allPackages) {
          TodoPackageNode packageNode = new TodoPackageNode(project, new PackageElement(module, aPackage, false), builder);
          if (!children.contains(packageNode)) {
            children.add(packageNode);
          }
        }
      }
    }
    final List<? extends VirtualFile> roots = collectContentRoots(module);
    roots.removeAll(sourceRoots);
    addDirsToChildren(roots, children, builder);
  }
@Override
  public void addPackagesToChildren(final @NotNull ArrayList<? super AbstractTreeNode<?>> children,
                                    final @Nullable Module module,
                                    final @NotNull TodoTreeBuilder builder)