Since it runs in HTML you should be at least able to either embed it within the window or reverse-engineer the HTTP requests. When creating a question, the terminal will display details of the information request, and while I haven’t yet attempted to try and use that in a custom implementation, you could likely use the logs to figure out what pieces are needed to generate the question form.
Also, the info on the development section would probably be of use to you. It explains how the .jar and Metabase program is structured and what they use in it. http://www.metabase.com/docs/v0.16.1/developers-guide.html