Why can't I command my civilians to go inside anymore? What happened!?!
The Dwarves Stay Inside order has been replaced by the more flexible Burrows and Alerts system. Basically, in ye olde days you'd have everybody stay inside, at which point they'd dance around the entrances causing job cancellation spam, getting in the way of the military, and generally being less than ideally protected, not to mention the bits where they'll hang out under a cliff and consider it inside, and I shudder to think of how this would have interacted with the caverns.
The idea in current versions is to make an emergency shelter for your dwarves. Like much of DF, planning ahead has big payoffs in terms of survivability, but if you're like me you'll just lay down a burrow on the meeting hall/food stockpiles when it comes up. Then, you assign that burrow to the Active alert via the military screen and set the civilian alert level from Inactive to Active. All nonmilitary dwarves will go to that burrow and ignore everything outside it.
Once you know what you're doing with it, you'll be making different fallback stages from "The currently excavated fortress" to "the meeting hall/bunkers" to "The emergency bunker, first dwarf in pulls the Lockdown Lever", and you'll be able to set up alerts to have your military do things like automatically deploy to different burrows (a burrow by the entrances to make dwarves defend the gates, for example) and so forth. It can be difficult to learn, but is amazingly flexible and quite useful once you get it- is true of the military screens in general, and DF as a whole, actually.