The "Custom CSS" and "Custom JavaScript" settings in the admin area allow you to paste CSS/JS code that will be appended t every page of the app:
You can use it not just to customize the look and feel of the app, but to call external APIs and hide unneeded elements from the user interface.
For example, add this line of CSS to hide the "Clone ticket" button from the ticket page:
#toolsPopup a[onclick="CopyTicket();"] {display:none}
You can also set "KB-specific" CSS and JavaScript that will be added to Knowledge-base pages only (for example if you need to add a analytics or tracking script like Google Analytics)
P.S. Please note that the app already loads jQuery, no need to include it again.