I didnt get too look at what crawford posted but i know that with the JVM you cannot make direct calls to the operating system. This means that the terminal clear code will not work. Also with the skipping lines, this leaves you at the bottom of the screen and most people do not want this. This leaves you really with only one way of doing it. Java has a class which allows you to call "Native classes" meaning classes written in different languages. This means you can write a class in C++ or C that clears the screen and make a call to it in java. Im working on this problem myself right now and am not exactly sure the way to go about it. Here is a link to a class that was already written by someone that will do it for u.
http://mimosa.snu.ac.kr/~danke/etc/ClearScreen.zip
I also found another way of doing it using ANSI code but it requires you to alter your config.sys file. This would then make the code machine specific. If you want this code too just let me know.