Coming back to this with thoughts. What you're describing sounds a lot like a menu tree.
"Press 1 to do this, 2 to do that, 3 to go to submenu A, 4 for B," etc. 1
"You have pressed 1. Do you want to turn on option ABC? [Y / n]" Y
"Do you want option QWERTY47? [Y/n]" N
"Are you sure you want to run notthebees --abc --no-qwerty47? [Y/n]" N
"Aborted."
It sounds like a standards problem waiting to happen because no two menus will be alike, but hey, things like this can and do exist, and setting one up isn't that hard, only time consuming.