Sandman
-- if (isset($backup_destination)){ exec("/bin/cp -R /home/$USER /mnt/$backup_destination"); } else { $backup_destination = prompt("Where do you want to backup to?"); } --

Few, if any, developers would call this a protocol. It's just conditional code. And I fear that nospam's suspicion was correct, you're way out of your league here because you're ignorant about the technical nature of these things. Maybe "protocol" is your way to make sense, in your head, for a series of steps taken by the software that you don't understand how it is done? No shame in that, you're in good company if you know nothing about the tech trivia of computers.

Eric Stevens
You should think in terms of a black box.

The protocol is an external set of requirements which determines what the black box is to do.

The program governs what goes on inside the black box which enables it to meet the externally imposed requirements of the protocol.

Note: The black box does not have to be a single box: it can include an operator. It can even be a building crammed with staff and computers. For the purpose of the discussion it defines a boundary around whatever it is that is intended to satisfy the requirements of the protocol.