The installation process of the Java-GI application template (a small "example" GNOME app built in Java) is now completely driven by Meson.
Flatpak-builder calls meson, meson calls gradle, gradle produces a "fat jar" (with the shadow plugin). Meson installs the jar and everything else (icons, settings, translations).
Link to the application template: https://github.com/jwharm/java-gi-app-template