В шаблоне:
JHtml::_('jquery.framework'); // до доктайпа
...
echo '<head>';
echo '<meta charset="utf-8">';
echo '<meta http-equiv="X-UA-Compatible" content="IE=edge">';
echo '<meta name="viewport" content="width=device-width, initial-scale=1">';
echo '<link rel="shortcut icon" href="templates/'.$this->template.'/images/favicon.png">';
echo '<jdoc:include type="head" />';
$doc->setGenerator('');
echo '<!--[if lt IE 9]>'.
'<script src="../js/ie8-responsive-file-warning.js"></script>'.
'<script src="http://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>'.
'<script src="http://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>'.
'<![endif]-->';
$scripts = $this->_scripts;
$this->_scripts = array();
$doc->addScript('/templates/'.$this->template.'/js/bs3.min.js');
$doc->addScript('/templates/'.$this->template.'/js/template.js');
$this->_scripts = array_merge( $this->_scripts, $scripts );
$doc->addStyleSheet('/templates/system/css/system.css');
$doc->addStyleSheet('/templates/'.$this->template.'/css/bs3.css');
$doc->addStyleSheet('/templates/'.$this->template.'/css/template.css');
echo '</head>';
Во фронте:
<link rel="stylesheet" href="/media/mod_order_present/css/mod_order_present.css" type="text/css" /> <link rel="stylesheet" href="/templates/system/css/system.css" type="text/css" />
<link rel="stylesheet" href="/templates/ceruleanai/css/bs3.css" type="text/css" />
<link rel="stylesheet" href="/templates/ceruleanai/css/template.css" type="text/css" />
<script src="/templates/ceruleanai/js/bs3.min.js" type="text/javascript"></script>
<script src="/templates/ceruleanai/js/template.js" type="text/javascript"></script>
<script src="/media/mod_order_present/js/jquery.validate.min.js" type="text/javascript"></script>
<script src="/media/mod_order_present/js/mod_order_present.js" type="text/javascript"></script> <script src="/media/jui/js/jquery.min.js" type="text/javascript"></script>
<script src="/media/jui/js/jquery-noconflict.js" type="text/javascript"></script>
<script src="/media/jui/js/jquery-migrate.min.js" type="text/javascript"></script>
<script src="/media/system/js/caption.js" type="text/javascript"></script>
Выделенное - надо в конец