private void buildOutputItemsList(
      final String outputDir,
      final Module module,
      VirtualFile from,
      final FileTypeManager typeManager,
      final VirtualFile sourceRoot,
      final String packagePrefix,
      final List<File> filesToRefresh,
      final Map<String, Collection<TranslatingCompiler.OutputItem>> results)
      throws CacheCorruptedException {
    final Ref<CacheCorruptedException> exRef = new Ref<CacheCorruptedException>(null);
    final ModuleFileIndex fileIndex = ModuleRootManager.getInstance(module).getFileIndex();
    final GlobalSearchScope srcRootScope =
        GlobalSearchScope.moduleScope(module)
            .intersectWith(GlobalSearchScopes.directoryScope(myProject, sourceRoot, true));

    final Collection<FileType> registeredInputTypes =
        CompilerManager.getInstance(myProject).getRegisteredInputTypes(myTranslatingCompiler);

    final ContentIterator contentIterator =
        new ContentIterator() {
          public boolean processFile(final VirtualFile child) {
            try {
              if (child.isValid()) {
                if (!child.isDirectory() && registeredInputTypes.contains(child.getFileType())) {
                  updateOutputItemsList(
                      outputDir,
                      child,
                      sourceRoot,
                      packagePrefix,
                      filesToRefresh,
                      results,
                      srcRootScope);
                }
              }
              return true;
            } catch (CacheCorruptedException e) {
              exRef.set(e);
              return false;
            }
          }
        };
    if (fileIndex.isInContent(from)) {
      // use file index for iteration to handle 'inner modules' and excludes properly
      fileIndex.iterateContentUnderDirectory(from, contentIterator);
    } else {
      // seems to be a root for generated sources
      VfsUtilCore.visitChildrenRecursively(
          from,
          new VirtualFileVisitor() {
            @Override
            public boolean visitFile(@NotNull VirtualFile file) {
              if (!file.isDirectory()) {
                contentIterator.processFile(file);
              }
              return true;
            }
          });
    }
    final CacheCorruptedException exc = exRef.get();
    if (exc != null) {
      throw exc;
    }
  }
  private void runTransformingCompilers(final ModuleChunk chunk) {
    final JavaSourceTransformingCompiler[] transformers =
        CompilerManager.getInstance(myProject).getCompilers(JavaSourceTransformingCompiler.class);
    if (transformers.length == 0) {
      return;
    }
    if (LOG.isDebugEnabled()) {
      LOG.debug("Running transforming compilers...");
    }
    final Module[] modules = chunk.getModules();
    for (final JavaSourceTransformingCompiler transformer : transformers) {
      final Map<VirtualFile, VirtualFile> originalToCopyFileMap =
          new HashMap<VirtualFile, VirtualFile>();
      final Application application = ApplicationManager.getApplication();
      application.invokeAndWait(
          new Runnable() {
            public void run() {
              for (final Module module : modules) {
                for (final VirtualFile file : chunk.getFilesToCompile(module)) {
                  final VirtualFile untransformed = chunk.getOriginalFile(file);
                  if (transformer.isTransformable(untransformed)) {
                    application.runWriteAction(
                        new Runnable() {
                          public void run() {
                            try {
                              // if untransformed != file, the file is already a (possibly
                              // transformed) copy of the original 'untransformed' file.
                              // If this is the case, just use already created copy and do not copy
                              // file content once again
                              final VirtualFile fileCopy =
                                  untransformed.equals(file)
                                      ? createFileCopy(getTempDir(module), file)
                                      : file;
                              originalToCopyFileMap.put(file, fileCopy);
                            } catch (IOException e) {
                              // skip it
                            }
                          }
                        });
                  }
                }
              }
            }
          },
          myCompileContext.getProgressIndicator().getModalityState());

      // do actual transform
      for (final Module module : modules) {
        final List<VirtualFile> filesToCompile = chunk.getFilesToCompile(module);
        for (int j = 0; j < filesToCompile.size(); j++) {
          final VirtualFile file = filesToCompile.get(j);
          final VirtualFile fileCopy = originalToCopyFileMap.get(file);
          if (fileCopy != null) {
            final boolean ok =
                transformer.transform(myCompileContext, fileCopy, chunk.getOriginalFile(file));
            if (ok) {
              chunk.substituteWithTransformedVersion(module, j, fileCopy);
            }
          }
        }
      }
    }
  }