Perform any necessary changes to the form values prior to storage. There is no need for this function to actually store the data.
Overrides HandlerBase::submitOptionsForm
public function submitOptionsForm(&$form, &$form_state) {
$form_state['values']['options']['format'] = $form_state['values']['options']['content']['format'];
$form_state['values']['options']['content'] = $form_state['values']['options']['content']['value'];
parent::submitOptionsForm($form, $form_state);
}