configureAndWatch does not close the configuration file making it impossible to 
change while running. The fix is as follows:
 public
  void doConfigure(String filename, Hierarchy hierarchy) {
    FileInputStream fis = null;
    try {
      fis = new FileInputStream(filename);
      doConfigure(fis, hierarchy);
    } catch(IOException e) {
      LogLog.error("Could not open ["+filename+"].", e);
    } finally {
      if (fis != null) {
        fis.close();
      }
    }
  }