Thank you for reaching out to us.
Indeed the jQuery Mobile sample app is no longer available as a project template but it is now listed as a demo app. You can read more about the new features and updates in the latest AppBuilder release in the Release Notes. Basically, to begin hybrid app development from the jQuery Mobile sample, you will now have to clone it in your preferred AppBuilder client - it is part of the Advanced APIs samples.
Let us know if we can further assist you.