You have to include jQuery before Javascript.js
<html xmlns="http://www.w3.org/1999/xhtml">
<head runat="server">
<title></title>
<script src="~/Javascript/jquery-2.1.1.js"></script>
<script src="~/Javascript/Javascript.js" runat="server"></script>
</head>
You said you have these errors in your developer console:
Failed to load resource: the server responded with a status of 404 (Not Found) localhost:46316/~/Javascript/Javascript.js
Failed to load resource: the server responded with a status of 404 (Not Found) localhost:46316/~/Javascript/jquery-2.1.1.js
Uncaught TypeError: undefined is not a function
You can fix these by setting the paths to your files correctly:
<html xmlns="http://www.w3.org/1999/xhtml">
<head runat="server">
<title></title>
<script src="/Javascript/jquery-2.1.1.js"></script>
<script src="/Javascript/Javascript.js" runat="server"></script>
</head>
Make IntelliSense work by putting this line of code to Javascript.js (as you realized yourself):
/// <reference path="jquery-2.1.1.js" />
Read the documentation of IntelliSense features and reference directives in here:
http://msdn.microsoft.com/en-us/library/bb385682.aspx#Features