In case you change the JavaBayes source code for some reason, note that all compiled classes should be placed in the Classes directory. You must set a flag in the Java compiler that directs output to that directory (use the flag -d); otherwise you will end up with class files mixed with source files. For example, you can go to the Source directory and type:
javac -d ../Classes JavaBayes.java
One thing you do not need to do is to install JavaCC, the parser generator that creates the parser in JavaBayes. Even though the distribution contains source files for JavaCC, there is no need to install JavaCC unless you want to modify the grammars for the parsers. In case you want to check JavaCC, you can obtain information about it with Metamata, the company that distributes it.
There are some issues that you must keep in mind: