Known: The generation of adamantine tubes and caverns is preseeded-rngdetermined at embark.
Found: If the embark square world tile savagery lowers a level during world gen due nearby sites, the above change. Adjacent tile savagery changes are ignored. Results in different underground geographies in year 1000 and 1500, for instance.
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Towers never attack generated sites during worldgen. However, post-worldgen they'll happily do it - usually ineffectually, but they can sometimes conquer a site. Oddly, they don't seem to suffer counterattacks for this, and can do it even if tower has only zombies in it. [insufficient testing of only 1 map, 2 years here]
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There's been a few mentions of nomadic necromancers. It's not been mentioned, so: a potentially nomadic necromancer can be pre-detected by them creating groups and then returning to a normal site,
like so, and during worldgen they're noticeable by typically popping 5-13 towers at once right after a war leaves some bodies lying in an open field.
This can get pretty ridiculous, should they swim over an ocean. Obviously, their upper cap is the number of groups they've created, so unlike normal necros century+ wait time between the provoking war and them becoming a necromancer is necessary.
They don't spam in response to direct attacks on sites, and usually (but not always) eventually settle down in their last tower, though there's low chance they may regress into visit site-create group-visit site pattern again, potentially caused by upgrading of a town.
Also, I'm speculating that they dislike other sources of reanimation for travelling (unproven, could very well be rng).
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It's rare, but caravans
can bring masterwork goods.
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Even if your cavern has no water, you may be able to still pour water in it and fish anyway.
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(Just like?) there can be dying dwarven civs with no real units but phantom ones in ęther, there can be major sites with phantom creature cap. Instead of shooting to 10k sentient population like expected, they shoot to somewhere like 5k or 7k or 3k, etc. and then stop and only slowly decrease from that number if not disturbed, never going above. Checked that they're not present in a camp somewhere else, either.
I believe these phantom units can be present from both before the town is even founded or after the dark fortress is created.
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Even if a tower has only zombies, it can still generate someone living to lead the assault on you. If you only get the living, this can give "a vile force of darkness has arrived" message, even if it is still tower sieging you right then and there.
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Towns won't experience population explosion until someone builds a sewer. Even if this population explosion looks like 80% goblins moving in from nearby dark fortress, none of them are moving into sewers, just appreciating the hygiene despite not eating or drinking.
Fortresses, oddly, seem to not apply immigration limits to animal people, even if they do the breeding limits:
1: Lolokral, "Granitesilvers", fortress
Owner: The Nets of Heaviness, dwarves
Parent Civ: The Immortal Helm, dwarves
1353 plump helmet men
1393 gorlaks
9 dwarves
39 humans
40 white stork men
1 goblin
111 magpie men
199 snail men
The biggest in numbers that I've seen, though hardly the most ridiculous in population/time.
Very rarely, something similar-looking, but different in that it always uses civilized races, can happen to forest retreats and hamlets as well:
22: Thiwacovema, "Bowedjungles", forest retreat
Owner: The Deer of Infamy, elves
Parent Civ: The Sun of Ransacking, elves
3973 goblins
1 dwarf
88 elves
673 goblin outcasts
5 elf outcasts
Both of those are in same 4200 year world gen, along with another less-ridiculous retreat and and hamlet (for hamlets and fortresses, seen them in other worlgens as well). I'm unsure what's the cause.
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E: Oh yeah, another one I forgot:
To solve the issue of "I want every z of my aboveground fortress have engraved obsidian floors, but when I dig cast obsidian it replaces that z with natural floor", you can cast above, dig away and then cave-in on top of a constructed floor resting on top of a support, replacing the constructed floor. Then you can deconstruct the support, keeping the obsidian floor on z-level right below.