Move CSS and JS cache folder
I'm not saying this is the best or correct way to do it, but I think you could use hook_file_url_alter to change the url for your script and stylesheets:

 function hook_file_url_alter(&amp;$original_uri) {
      // rewrite url for your javascript files
      if(strstr($original_url, 'sites/default/files/your-script.js')) {
          $original_url = 'http://example.com/js/your-script.js';
      }
 }