using android aapt in java program-Collection of common programming errors

Old question, I know, but try this out:

String[] cmd = {"aapt", "package", "-u", "-f", "-F", "/"//home//jay//testing_FILES.apk/"", "/"//home//jay//testing_FILES/""};

Runtime run = Runtime.getRuntime();
Process pr = null;
try {
    pr = run.exec(cmd);
    pr.waitFor();
} catch (IOException e) {
    e.printStackTrace();
} catch (InterruptedException e) {
    e.printStackTrace();
} finally {
    if(pr != null){
        close(pr.getOutputStream());
        close(pr.getInputStream());
        close(pr.getErrorStream());
        pr.destroy();
    }
}