JLS

Fixed read regression from last night. Currently, there remains an issue reading in zipped JLS files, but not plain text or xz'd files. However, this issue may be related to an underlying bug as it doesn't always appear, available text ends early and unexpectedly, and input text is valid.

I think I finally got rid of the .class files.

Still trying to get rid of the .class files.

Fixing reading from files not in the program directory

resolved code merge conflicts, somehow binaries were re-introduced.