we have forked IntelliJ IDEA community edition (15) to make it a bit easier for our users to get up and running, see http://robovm.com/robovm-1-4-released-robovm-studio/ and https://github.com/robovm/robovm-studio.
Our build process is essentially a duplicate of the Gant files in build/ (see build-robovm/). Everything works pretty great, but i'm not in the process of getting proper versioning going.
It appears that versioning is spread across multiple sites in IntelliJ IDEA. I managed to modify various files like ApplicationInfo.xml, build.txt etc. to have a somewhat working versioning scheme. It's all very hackish though, and some things don't work (e.g. build.txt must follow a specific syntax, otherwise the platform fails with a parsing error on startup).
Since other JetBrains products are based on this app platform, i'm sure there's a streamlined process to modifying the versioning scheme. I'd be super greatful if you could offer some insight into how this works!