Usually, in Visual Studio you can use reference directive in the beginning of the file. It will include a script file in the scripting context of the current script file. And IntelliSense will be enabled. Since WebMatrix is microsoft as well, I believe this should work too:
/// <reference path="JS/jquery-2.1.0.js" />
/// <reference path="JS/jquery-2.1.0-vsdoc.js" />
if path attribute won't work, try file attribute.