They should all be mushrooms or some other sort of fungi. Plants need photosynthesis, not really possible underground. I would like for underground farming to be made less easy so above ground farming can provide a wider range of better crops; for example, the sugar needed for brewing would have to come from overground sources.
Above ground farming is not something that AI dwarves actually do, if you do it in the game then you are actually innovating. I think that underground farming should be enough to sustain a dwarf population and above ground farming should not be needed at all.
Sugar is not needed for brewing. Yeast is needed for brewing and the yeast feeds on the sugar that exists in the plants or fruit you are brewing. Normal mushrooms are digestible into sugar, but not easily enough for the likes of yeast to feed on. There are three possible ways out for this problem.
1. Dwarf underground plants are actually fungal fruit, something that does not exist in reality but could have existed theoretically. The fungal growths that the dwarves grow are meant to be eaten, releasing the spores within. To this end they, like surface plants have easily accessible sugar in them.
Actually real-life mushrooms with sugar in them actually exist.
http://www.ajofai.info/Abstract/Evaluation%20of%20rare%20sugar%20content%20from%20edible%20mushroom.pdf2. Dwarves have access to some kind of mushroom eating yeast, something that does not exist in reality but could have existed theoretically. This yeast digests the mushrooms down into sugar but will also grow quite happily in normal sugary environments as well.
3. Dwarf 'alcohol' is actually
Psilocybin.
Yes but not all underground stuff is fungus. And even if they were, fungi still need to get energy from somewhere. If it's not sunlight, it needs to be something. You can't just wet a rock and grow stuff on it or keep using the same soil forever.
However, you don't need to introduce poop to make fertilizer. Having the animals graze over fallow fields - like I said a few pages ago - would work the same way without poop ever making an appearance.
I agree that clutter is a big problem but I'm sure some sort of recycling will be put into place sooner or later. Metal stuff can be melted already, corpses rot and you can use the bones and skulls.
Maybe one day we'll be able to build out of bone like some chapels, tattered clothes can become rags for hospitals and wooden stuff can be used to make fires everywhere if dwarves being cold in the winter ever becomes a thing.
Other than that, you can have an incinerator where you burn everything you don't need.
And really a moat is the easiest thing in the world to make, just channel out a few tiles outside somewhere and designate as pooping grounds. Later on, when you can build pipes, toilets and pumps you can have the sewer system dump it there.
EDIT: Oh and pooping outside = bad thoughts. Pee pots are better which they then empty in appropriate places. Holes in the floor in a bathroom are one step above. Toilets are the decadent luxury.
It would not work because animals cannot graze over your underground farms since there is nothing there to graze on. Additionally there is no new energy content into the system to solve your problem, the animals eat the fungi that is there and they recycle only the energy that they have consumed in the first place.
Clutter is a major problem in the game and yes recycling is needed in general; your various ideas for dealing with clutter are not a denial of the problem. Adding sewage without soil nutrients and fertilisation to go with it is adding to the lack of recycling/clutter problem, adding it alongside soil nutrients however allows us to introduce both the problem and the solution to the problem at the same time.
The problem you are describing actually is generally however not a real one if we are talking about the surface layers. That is because nutrients from the surface are constantly dripping down into your farming area. The amount this happens would actually be decided by the rainfall of the area. In an area that gets constant rainfall, your plots will be constantly replenished by nutrients dripping into your plots from the surface level.