the new military (mainly because i havent figured it out yet), and not having the order: "dwarves stay in-doors"
When you figure it out you will probably
love not having the order "dwarves stay in-doors". What's replaced it is so, so much better.
Basically, you define a burrow that encompasses all the parts of your fort that you consider "safe", and then you assign that burrow as the civilian safe zone for each of your various alert states. Then when you put your squads into that alert state, just set that alert state to your civilians too. Everyone will drop everything and run to the bunker.
I have yet to experiment extensively with this setup but the possibilities are wonderful. I'm just starting my first "real" fort, devoted to more than just messing around, and I plan to set up a graded response. There will be a burrow that fills pretty much all of my fort's interior, not including the corridors behind the arrow slits. This will be the safe zone for protracted sieges and should allow my dwarfs to go about their everyday lives as best as possible during them. There will be a smaller burrow nested inside that which encompasses just a dorm, a food stockpile, and the hospital zone; this will be for if the enemy breaches the outer layers of my defenses and gets into the fort proper. And if all else fails, I'll maybe have a "Jonestown Bunker" where I can have my civilians retreat to and wall themselves in to die in peace.
Once I breach the lower caverns I think I might move my fort down there entirely, in which case I'll create safe zones down there as well. Though I'll keep the surface installation in mothballs, that way if I'm attacked from below I can order my dwarfs to the safety of the surface.
Finally, above-ground fortifications can be
habitable during a siege. I could even make a walled city with individual buildings scattered around and it'll work.