undefined method Phalcon\Flash\Direct::output()

You did mistake, should be

$di->set(
    'flashSession',
    function () {
        return new Phalcon\Flash\Session(array(
            'error' => 'alert alert-dismissable alert-danger',
            'success' => 'alert alert-dismissable alert-success',
            'notice' => 'alert alert-dismissable alert-info',
        ));
    }
);

or

$di->set(
    'flash',
    function () {
        return new Phalcon\Flash\Direct(array(
            'error' => 'alert alert-dismissable alert-danger',
            'success' => 'alert alert-dismissable alert-success',
            'notice' => 'alert alert-dismissable alert-info',
        ));
    }
);