12. It just seems like something very simple to do.
MS-DOS just translates very basic machine code (hex or binary) into something accessible with alphanumeric language humans can understand. MS-DOS was primitive and easily replicable. If the NSA had a program to develop a new base language using completely different command structures then only those with an understanding of the fundamentals of the language would have the ability to access the system as a whole. What could it cost? An educated "hacker" with an interest in such things could do it himself. A team of 5 could do it for a million dollars. A team of 100 could do it for 100 million and make it impenetrable.
I really thought I read somewhere that the Pentagon uses its own system. There must be a way to make a document readable only on one OS. As long as the fundamentals of how the OS works are kept secret.