For each of the library package * the source should be somewhere in package/src * pre-compiled classes in package/classes * classes instrumented by cobertura in package/iclassses Cobertura instrumentation need to be done only once; and this has been done now. If we ever need to instrument again, use older Java for that! The command-line instruction at Cobertura site does not work, I used: java -cp "c:/apps/cobertura/cobertura-2.0.3.jar;c:/apps/cobertura/lib/*;./classes" net.sourceforge.cobertura.instrument.Main --destination ./iclasses classes