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JavaScript working in debugger but not when published to IIS

I have a few scripts that work fine running in the debugger, but when I publish it to IIS it's like they aren't running.

Here are the lines i'm using to include the scripts inside the head tags

<script src="http://ajax.googleapis.com/ajax/libs/mootools/1.2.4/mootools-yui-compressed.js"></script>
<script src="<%=ResolveClientUrl("~/Scripts/")%>ScrollSpy.js"></script>

scripts are contained in Scripts folder

Correct me if I'm wrong but it sounds like you can't debug Javascript in VS? If so, have you considered using browser based debugging tools? Chrome, Firefox, and IE 11 have pretty great debugging tools that allow you to set breakpoints just like in Visual Studio.

There's a free course online that'll teach Google Chrome's DevTools at Codeschool - http://discover-devtools.codeschool.com/

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