I am going to need standard input for the AOT JAR processing, but this should not be hard to do. At least doing the AOT over standard pipes makes it the easiest to use and it could be done as a stream.
Also so glad I did the refactor on the Gradle tasks and such, this is making the AOT part much easier. Also this is much easier and handles better than the previous build system compilation. At least with the AOT modules I will be able to use those directly from within SquirrelJME to compile things naturally.