Is there a way that I can make my program in java, but make all of the plugins lua based? How can I do all of the hooks and such across the languages and can I access the functions and such from Java? I would prefer if this were to be done during runtime as opposed to having a cross-compiler that changes it beforehand.
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One alternative is LuaJava. It allows you to use Lua scripting in Java program. Speaking literally about implementing interfaces in Lua:
An example of such implementation:
Of course, you can also call “normal” Lua functions from Java, using the familiar C API (adapted to Java).