File srcTemp=new File(tempClassFile.getPath()+File.separator+"src");
srcTemp.mkdir();
copyDirectory(new File(output.getOutputLocation()+File.separator+"src"),srcTemp);
//Compile the source to another directory
SrcCompiler srcCompileTool = new SrcCompiler();
srcCompileTool.compileSource(tempClassFile.getPath());
//create the jar file and add that to the lib directory
String projectLib = output.getOutputLocation()+File.separator+"lib";
JarFileWriter jarFileWriter = new JarFileWriter();
String jarFileName = "CodegenResults.jar";
if (!output.getJarFilename().equals("")){