A related question: Would it be possible to have the game update changes to the raws in real time (for stuff that don't require a regen) or would it require a save, quit application, reload application, reload save anyway due to the way the code works? Or maybe that could work better for the arena itself since it doesn't have to load the raw for everything that exists.
Creatures build their data according to the raws, but a lot of it is stored inside of them if it can't rely on the loaded raw definition. Keeping track of which variable is which type would make adding that kind of thing sort of a mess. It's more straightforward for things like weapons, maybe, where the data from the raws all remains in the loaded raw definition. It's still a project though, because it has to clean up and copy over the old raws without messing up anything that's dependent on the current instance of the raws, and those dependencies are potentially all over the place.
I was mostly curious if you thought of a way to handle them and how are you even going around to do it?
You also seem to want more then them to simply die off but also to leave behind explorable structures. Are you going to just give them some sort of odd "Hoarding, Ghost Transforming, Dungeon Building" Culture unique to the "Extinctified cultures"?
I think it would be sort of odd to add an entity def that is bound for ruin. As the currently released version stands, there are ruins of old structures that come from sites that happened to become unpopulated in some way. So if you were to find pyramids like the old ruined pyramids from the older 3D versions, they would have come from a pyramid-building civilization you could just as easily find alive. You can currently find a ruined keep in that way (from a civ that would have an occupied keep). The current entity defs just need more diversity than they currently have.
I don't think it's crucial to have dungeon-type locations that are left behind with level-graded treasures scattered properly or something like that (the pyramid ruins were like that -- it hid the best stuff deeper in). If there are dungeons, they'd be either abandoned or occupied, created in world gen or during play by the sort of critters that would have a dungeon (like a dwarf fortress). Game-wise, it would certainly be better to have the old 3D zombie ruins from before than nothing, but hopefully we can do better than that. Ideally, every explorable adventure location that you find would have a real reason for being there, linked in with the world history and everything else. There are plenty of ways for that to still involve interesting things to find laying around, though places that would have been looted by whoever sacked them and so on should probably be looted.
Ghost transformations are one of those metaphysical matters that didn't have explanations attempted in the game when they existed, just like the current undead regions. When those have explanations, things like ruins with zombies should arise more naturally. This could involve gods in pantheons of death/rebirth/etc., regions linked to death/etc. for whatever reason, etc., but it's all specific mechanics at that point. I guess a key point there would be that site/civ-wide zombie transformations would still theoretically be able to happen during play, which would be cool, once you've got the world gen mechanics trickled over to dwarf mode or adv mode (or vice versa, whichever way it goes in first).
All of that said, back in the old Armok, there was a notion floating around linked to world generation parameters of being able to attach plot notions to your world. Looking now at dwarf world gen, it might be hard to jam a notion like "world must have an ancient, dead civilization with stuff" into it while maintaining the current system of having a timeline move forward, but it's possible to get away with things like that by, for instance, picking a civ to have crappier and crappier luck until it finally hits the deadline and, if the civ is still alive, it drops an apocalypse. I dunno if the priorities will shift that way though.