Sorry for not checking in a week or two...
Underground plants could be just fungus + unique biolog, thats it, fictional and probably not real life working biology but with a biology with some defined rules and be it.
Thing is, there are also magical above-ground plants, such as that eyestalk grass in evil biomes, as well as feather trees in good biomes, or whip vines in savage biomes. The point of the system is to unify it all into something extensible, so that the cavern biomes run by the same sort of rules as the magical surface biomes.
It's just that a magic-less surface is a mundane plant and animal surface, while a magic-less cavern is almost certainly barren except for a small amount of possible mushroom farming that depends upon pulling down nutrients from living creatures that would have to either come from the surface or a magical area.
Again, it might not be strictly necessary, but especially with the system of a sliding scale of magical-ness, as well as the procedural magical fields, a more modular and comprehensive system for magical environments and how they interact with individual populations makes for a more believable magic world.
I think that the dwarves would gather up the fallen leaves in the autumn en-masse for their underground gardens too. If dwarves did poop they would also recycle it into fertilizer for said gardens too, but presently they don't .
How about procedurally generating magical versions of both surface and underground plants, using the mundane plants as the base; as opposed to having to raw-define individual magical plants for every single random magical biome. Like a lot of these things we need to have defined active words, so instead of us getting fiery plump helmet, we have plump fires or fiery helmets for instance. The magical biome itself feeds an energy to the magical plants, which will die if removed from that biome, but compete with other plants over the biome leading to a maximum density of said plants making room of the mildly magical biomes for regular plants to grow.
I agree however with LordBaal that the magical requirement should be an additional requirement on top of the normal mundane requirement because we need some challenge for the player in maintaining nutrient levels AND while possible it is far too much work for the poor devs to make unique rules for the energy in the other biomes that provides equivalent challenge, by which I mean something other than the environment itself feeding things energy. Another thing to consider is the situation in regard to caverns or lands *of* fertility, in that case I would imagine the 'magical' plants would simply be super nutrient hungry (and nutritious) but live in an environment where nutrients simply get magiked in.
Yes, I have
a list of potential fertilizer sources (second section), including dead leaves and even things that can be mined (although such things would be quite finite) and discuss the use of sewage as fertilizer ("night soil").
And as mentioned in my response directly to LordBaal, the idea is certainly that of a mundane set of reactions, plus, whereever there is the option for magic, those magical plants and creatures exist, as well. Especially if we're building this around the notion of five different settings in a "magicalness spectrum" from mundane to full-on wacky everyone's-from-a-procedural-species-which-spits-water-streams-and-can-turn-their-hands-into-hammers where magic is presumably overwhelmingly omnipresent. In the latter case, there would probably need to be some sort of mechanic for outcompetition, where either everything becomes mutated into magical versions of mundane things or mundane species go extinct if magic simply IS so omnipresent that magic out-competes the sun as an energy source in those areas. (That said, even in the max-magic worlds, it seems like magic will be localized, so it would be like a barren ocean floor suddenly becoming a brilliant coral reef when you get to the shallows near a lagoon.)
Using some sort of modular system where any sort of living creature (or even some inanimate ones) suddenly becomes a sphere-aligned variant is definitely the sort of thing I advocate. You can just look at how all the giant critters work, and you can see how there are so many things that individually statting them out is silly, and Toady just made a pseudo-procedural method of creating giant creatures. (Although there had been some bugs with even that, due to unforseen consequences of things like giant mosquito swarms when a giant-ification was placed on vermin...) Undead basically work as a decent example of purely procedural creature modification.
The thing is, you need to come up with sane ways for all the different spheres to work. They're not just plain-and-boring Greek elements like water where you can just add some sort of elemental attack and passive elemental resist like a paint-by-numbers RPG does, you have spheres for things like Music, Dreams, War, Honor, or Wealth. Making mechanics for musical creatures or honor creatures would presumably take more care and creativity than that. (I spend a good deal of time on the topic, also trying to get people to suggest some in the
Xenosynthesis thread proper.)
Of course, if you want to have creatures made of what should biologically be inanimate objects, like amethyst men or the like, then you probably need to have special instances, unless you want to make it like Titans/Forgotten Beasts where you can have whole species of things made of (paper) sheet music or steam or something that shatter at a funny look in some locations, and have whole fields of solid steel critters in others. Granted, we don't need to worry about "competitive balance" in Dwarf Fortress, but things shouldn't be completely ludicrously broken where the first simple magic bunny rabbit is a fortress-ending threat on par with a titan in some zones, while making other zones utterly defanged. (Especially since the xenosynthesis mechanics pretty much directly invite players to deliberately screw with the magical balance to suit their whims.)