Update scripts folder that get added into a new asp.net web application

I think you have to define your own project template (or edit the existing one). In the .vstemplate file you have a section where you can define which packagaes have to be installed when creating a new project with this template. If you have a look at the Asp.net MVC template you see that there are a few packages defined which are installed by Nuget.

<WizardData>
        <packages>
            <package id="jQuery" version="1.5.1" />
            <package id="jQuery.vsdoc" version="1.5.1" />
            <package id="jQuery.Validation" version="1.8.0" />
            <package id="jQuery.UI.Combined" version="1.8.11" />
            <package id="EntityFramework" version="4.1.10331.0" />
            <package id="Modernizr" version="1.7" />
        </packages>
    </WizardData>
</VSTemplate>

In this template there is a version defined for jquery, but if you remove this version number than Nuget will automatically install the latest version of JQuery which is right now something like 1.6.1.

To be honest I never have updated or created a new template, so for the exact steps I can only give you the references. Hope that this will guide you into the right direction:

Creating a new project template: http://msdn.microsoft.com/en-us/library/ms247065.aspx

Existing templates can be found in the following location: C:\Program Files (x86)\Microsoft Visual Studio 10.0\Common7\IDE\ProjectTemplates

I think only Nuget has the option to check for the latest version of JQuery to download, using a CDN would require a version number.

Hope this will help you.