code: private boolean isSpecialFlagSet(final OptionSet parsedArguments, final String flagName){
          if (parsedArguments.has(flagName)){
              Object value = parsedArguments.valueOf(flagName);
              return  (value == null || !value.equals("false"));
          } else{
              return false;
          }
      }
docs: helper to deal with the case of special flags that are evaluated before the options are properly set