call js in html.tpl.php
Its too simple my friend. For these types of manipulations template_process_html(&amp;$variables) comes handy. This is provided by theme.inc located in includes/ folder of your drupal directory.

You can put this function in your template.php file of your custom theme directory

/**
 *Implementing template_process_html()
 */

function custom_theme_process_html(&amp;$variables) {
    $path = drupal_get_path('theme','custom_theme');
    $variables['scripts'] .= '&lt;script src="' . $path . '/js/jquery.smoothState.js"&gt;&lt;/script&gt;
&lt;script src="' . $path . '/js/functions.js"&gt;&lt;/script&gt;';
}



  This will append these new scripts to your scripts variables that is rendered to html.tpl.php as &lt;script&gt; tags while processing it. Provided that you put these scripts in the js folder located in your theme folder . So the file path should be like this - sites/all/custom/themes/custom_theme/js/functions.js.


Don't forget to clear the cache as its a new hook in your template.php file and drupal won't execute that hook until you do that.

Hope that helps.