cl.addOption("-indir",inDir,"The input directory");
cl.addOption("-of",outDir,"The output directory");
cl.addOption("-r",recursiveFlag,"Recurses through all subdirectories.");
cl.addOption("-skip",skip,"Skips the specified directory.");
cl.parseArgs(args);
if (ofn.length() > 0){
try {
out = new BufferedWriter(new FileWriter(ofn.toString()));
} catch (IOException e) {