I find that cloneit x y z is more intuitive than cloneit x,y,z. A destination path would then be provided through a flag instead of as the second argument (--output or --dest maybe?).
As I'm writing this, I've actually thought of another possible solution: take the last argument (assuming there are 2 or more arguments provided), check if it is a URL (parse it and check if it has a certain protocol), if it is, download as normal, if not, interpret it as the destination path.