HADiT requires Java Development Kit (JDK) 1.5 or higher in order to compile. Assuming that the source code is in the directory $PROJECT_DIR/src, the libraries are in $PROJECT_DIR/lib, and you are in the source code directory, the command to compile the source code, as well as link in the libraries, on UNIX systems is:

javac *.java -d ../bin/ -classpath .:../lib/commons-math-1.1/commons-math-1.1.jar:../lib/jfreechart-1.0.6/lib/jcommon-1.0.10.jar:../lib/jfreechart-1.0.6/lib/jfreechart-1.0.6.jar:../lib/jfreechart-1.0.6/lib/jfreechart-1.0.6-swt.jar:../lib/colt/lib/colt.jar:../lib/colt/lib/concurrent.jar
The class files will be placed in the $PROJECT_DIR/bin directory (make sure you create it before compiling).