Burrows: easiest way of getting the meat of the old 'dwarves inside' order is to create a burrow over the food and drink stockpiles. You'll get a ton of cancellation spam, but it doesn't seem to cancel anything at the workshops and you only have to deal with it until the fortress can be sealed properly.
Assuming that you haven't touched the burrow or military screens at all --
[w], [a], Enter. That takes you to the screen where you set the burrow's location. Create the burrow using the Enter and movement buttons (ie. like a stockpile). You can do this as many times as you like and the squares don't need to be connected, or even on the same z-level. Hit Escape twice to return to the main screen. Next...
[m], [a]. Alerts are to the left, burrow list to the right. The default civilian setting is Inactive, which refers to your dwaves and not the alert itself or anything (it should probably be called something less ambiguous). It starts out with a bright green [CIV] next to it. The Burrows column will have one name in it, and that will be Burrow 1. Hit right, press Enter, and a green A will appear next to the burrow name. Pressing Enter again will cancel the alert, but don't do that yet.
Once you return to the game, all your civilian dwarves will move to the area you specified. If you cancel the alert right away, they'll carry on to the burrow regardless.
The advantage of burrows is that they don't just do 'dwarves go inside'. You can also do 'dwarves go up beyond the reach of flooding' or whatever, and assigning a single dwarf to a burrow lets you force them to use a particular stockpile without the hassle of physically locking them in. I think the way to use the system fully is to create a burrow for each industry so that you can have a sprawling fortress but still keep your skilled workers in the general area of their workshops. But since you can't have a bunch of small food stockpiles drawing from a central one you're still going to have to figure out how to keep all your burrows stocked or put up with dwarves wandering back and forth for food and drink.
Question for everyone else... is this loss of grasping always an indicator of nerve damage?