timeout should be applied to stories only

    public void waitUntilAllDoneOrFailed(BatchFailures failures) {
        long start = System.currentTimeMillis();
        boolean allDone = false;
        while (!allDone) {
            allDone = true;
            for (RunningStory runningStory : runningStories.values()) {
                Future<ThrowableStory> future = runningStory.getFuture();
                if (!future.isDone()) {
                    allDone = false;
                    long durationInSecs = storyDurationInSecs(start);
                    long timeoutInSecs = embedderControls.storyTimeoutInSecs();
                    if (durationInSecs > timeoutInSecs) {
                        Story story = runningStory.getStory();
                        StoryDuration storyDuration = new StoryDuration(durationInSecs, timeoutInSecs);
                        embedderMonitor.storyTimeout(story, storyDuration);
                        storyRunner.cancelStory(story, storyDuration);
                        future.cancel(true);
                    }
                    break;
                }