Hah! Only found out afterwards that there is actually a project that sync’s the ImageJ source with a proper Maven project setup: ImageJA.
Furthermore, there is also ImageJ2 in the pipeline, a rewrite from scratch to have a more modular project structure while trying to maintain compatibility with the old ImageJ. Oh well, doesn’t hurt to have it available from multiple sources. 😉 Will get published on Maven Central at some stage, I guess.