IOS – Is it possible to upgrade iOS offline

You can install OpenSSH in Cydia and use a SSH client (say, Panic's Prompt - look for it in the App Store), that makes a pretty nice terminal emulator for iOS.

As to running programs from the command line, sure, no problem, but none of them are designed to work in CLI. They don't retrieve/parse arguments, don't output...etc If you can get some out of Cydia or compile them yourself, it'll work, but I don't think you'll be able to command Apple's own apps that way.

This YouTube video on Semi-Restore iOS 6.1.2, 6.1.1, 6.1, 6.0.1, 6.0 iPhone 5, 4S, 4 definitely works. It worked for me.