For compiling Java code with MUSCLE, the Java archives in $MUSCLE_HOME/share/muscle/java and $MUSCLE_HOME/share/muscle/java/thirdparty should be added to the classpath. MUSCLE automatically includes these in the class path when running. To get these files formatted as a classpath, run

muscle2 --print-env=CLASSPATH

Modify the classpath of MUSCLE to add your own dependencies by adding the following lines to the configuration files

m = Muscle.LAST
m.add_classpath "path/to/dependency1.jar"
m.add_classpath "path/to/dependency2.jar"

The INCLUDE_PATH for C and C++ should include $MUSCLE_HOME/include, and the library path should include $MUSCLE_HOME/lib, specifically the $MUSCLE_HOME/lib/libmuscle2.so or $MUSCLE_HOME/lib/libmuscle2.dylib (depending on the operating system).