private void appendChosenAnnotationsRoot(
     @NotNull final OrderEntry entry, @NotNull final VirtualFile vFile) {
   if (entry instanceof LibraryOrderEntry) {
     Library library = ((LibraryOrderEntry) entry).getLibrary();
     LOG.assertTrue(library != null);
     final ModifiableRootModel rootModel =
         ModuleRootManager.getInstance(entry.getOwnerModule()).getModifiableModel();
     final Library.ModifiableModel model = library.getModifiableModel();
     model.addRoot(vFile, AnnotationOrderRootType.getInstance());
     model.commit();
     rootModel.commit();
   } else if (entry instanceof ModuleSourceOrderEntry) {
     final ModifiableRootModel model =
         ModuleRootManager.getInstance(entry.getOwnerModule()).getModifiableModel();
     final JavaModuleExternalPaths extension =
         model.getModuleExtension(JavaModuleExternalPaths.class);
     extension.setExternalAnnotationUrls(
         ArrayUtil.mergeArrays(extension.getExternalAnnotationsUrls(), vFile.getUrl()));
     model.commit();
   } else if (entry instanceof JdkOrderEntry) {
     final SdkModificator sdkModificator = ((JdkOrderEntry) entry).getJdk().getSdkModificator();
     sdkModificator.addRoot(vFile, AnnotationOrderRootType.getInstance());
     sdkModificator.commitChanges();
   }
   myExternalAnnotations.clear();
 }
  private static boolean changePackagePrefixes(
      PsiPackage psiPackage, final String oldQualifiedName, final String newQualifiedName) {
    final Module[] modules = ModuleManager.getInstance(psiPackage.getProject()).getModules();
    List<ModifiableRootModel> modelsToCommit = new ArrayList<ModifiableRootModel>();
    for (final Module module : modules) {
      boolean anyChange = false;
      final ModifiableRootModel rootModel =
          ModuleRootManager.getInstance(module).getModifiableModel();
      for (final ContentEntry contentEntry : rootModel.getContentEntries()) {
        for (final SourceFolder sourceFolder :
            contentEntry.getSourceFolders(JavaModuleSourceRootTypes.SOURCES)) {
          final String packagePrefix = sourceFolder.getPackagePrefix();
          if (packagePrefix.startsWith(oldQualifiedName)) {
            sourceFolder.setPackagePrefix(
                newQualifiedName + packagePrefix.substring(oldQualifiedName.length()));
            anyChange = true;
          }
        }
      }
      if (anyChange) {
        modelsToCommit.add(rootModel);
      } else {
        rootModel.dispose();
      }
    }

    if (!modelsToCommit.isEmpty()) {
      ModifiableRootModel[] rootModels =
          modelsToCommit.toArray(new ModifiableRootModel[modelsToCommit.size()]);
      if (rootModels.length > 0) {
        ModifiableModelCommitter.multiCommit(
            rootModels, ModuleManager.getInstance(rootModels[0].getProject()).getModifiableModel());
      }
      return true;
    } else {
      return false;
    }
  }