If you want to put your pages into subfolders you will need to alter the path to the plugins so the script.js file can find them correctly. To do this (since AppStrap version 3.0.5) you can simply add the following to the body tag for all pages that are within subfolders:
<body data-plugins-localpath="LOCAL-PATH"> If you pages is within 1 subfolder (/admin) it would look something like:
<body data-plugins-localpath="../assets/plugins/">you can also use the absolute domain path to like:
<body data-plugins-localpath="http://example.com/assets/plugins/">