We used to have a tutorial on bundling a java app, but dropped it when we moved the docs - the tutorial wasn't getting maintained and had got out of date.
We might want to bring the tutorial back, although we'd need to make sure that it got maintained in the future.
The latest version of the tutorial can be seen here:
https://github.com/flatpak/flatpak.github.io/blob/81bb006fd96b9a13170bd876316eb5a4eb48244b/source/bundling-a-java-app.html.haml.markdown