The two lines must remove the Joomla 3 minutes and add to the bottom line instead:
// Add JavaScript Frameworks
JHtml::_('bootstrap.framework');
// Load optional RTL Bootstrap CSS
JHtml::_('bootstrap.loadCss', false, $this->direction);
This line of Joomla 2 is to be replaced:
$doc->addScript('templates/' .$this->template. '/js/jquery.min.js');