Remove unnecessary native parts

[nvcleemp]

There are several parts that make use of JNI, but can be replaced by regular Java these days. At some point we should refactor out these parts. E.g., in many places the code actually expects an EmbeddableGraph to be a NativeEmbeddableGraph. I think the main reason there originally was to use JNI was to run external processes. This can be done with plain Java these days.