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RotP is open source, improve it all you want.
I have implemented Maven build system in the Governor mod, so you're welcome to fork from my codebase and extend it. Modnar has done so. https://github.com/coder111111/rotp-public
In case you have existing low level code in C/C++ and you want to integrate it with Java, there's https://github.com/java-native-access/jna But it's fairly unwieldy to work with, and calls Java=>C carry an overhead, so you want as few of them as possible. Which in ROTP means you want to transport all the relevant data into your AI code, then do the processing on a handful of calls, then return the result. Alternatively, an option would be to export say savegame (or other data) as JSON, run your AI module as a separate process, and then write the results to another file. While ROTP at the moment cannot do JSON save games, I have begun looking into it.