There is no difference at all. They probably want you to use emacs and use the command line to compile Java source without using a more 'user friendly' IDE (integrated development environment) - so you understand a little more whats going on.
Historically IDE's were only really available with Windows - this is going back some years. Being a Uni most of the lecturers will be stuck in the 60's. Have they mentioned "in our day we coded on punch cards..." yet?
However, times move on...and Linux has just as good GUI and IDE's now. Infact, all of the free ones available on Windows (Eclipse, NetBeans) came out of Linux anyway.
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