First disable editor: System -> Global configuration -> Default Editor: Editor - None -> Save
Then when you upload some script, or jquery file, in my case you can use it like this:
<script type="text/javascript" src="http://www.milosev.com/Download/dontLooseFocus/jquery-2.1.3.js"></script>
But when you use jQuery in your article, then you have to use jQuery instead of "$", for example:
jQuery("#myText").val("");