Not able copy apk to system-priv app folder using shell command in java android

Question

I'm having difficulty copying a apk from the /data/app folder to the system/priv-app in my app. The device is rooted and i can copy to other folders just not the system folder.

I have also tried copying my app to the system/priv-app folder and still not able to copy.

I can copy using adb and it works fine.

adb root
adb mount -o rw,remount /system
adb cp -r data/app/packagename system/priv-app/packagename
adb reboot

here is my code in java

Runtime.getRuntime().exec("cp -r /data/app/com.test.myapp /system/priv-app/MyApp");

I have also tried other libs to check if the device is rooted and they all report rooted but yet a simple task like this fails with

java.io.IOException: write failed: EPIPE (Broken pipe)

try
{
    Process p = Runtime.getRuntime().exec("su", null, new File("/"));
    DataOutputStream os = new DataOutputStream( p.getOutputStream());
    os.writeBytes("pwd\n");
    os.writeBytes("exit\n");
    os.flush();
    p.waitFor();
    p.destroy();
}
catch (Exception e)
{
    return false;
}

Do I need to give the app root owner?