Given an AnnotationScript instance, and two File, in and out, reads the class file from in, runs the
AnnotationScript on all InstructionLists in the class and then writes the annotated version to the
out file.
Given three File objects representing a annotation script file, class file to read, and a class file
to write to, builds an AnnotationScript instance, runs it on the given class, and writes its annotated
version.