Mandates requiring unavailable resources have always been a problem, but I see what you mean about it creating too big of a problem. I haven't had too much of a issue with it, though, I'd have thought being completely unable to acquire some varieties of wood except in small amounts by caravan or requiring a trojan pony attack would be a bigger problem. It'd be easy enough to put all painted woods onto one plant and change the reactions accordingly, I'll make an optional module for that. Should I differentiate between tree, conjured, ent and trojan wood? Just be aware that if I do I'll make rubberwood trees convert to painted trojan wood for a giggle.
As for castes, all you have to do is delete both male and female castes of a kind and their description data from the end of the creature file, and maybe rejig pop ratios. While I understand it may seem a bit much to do it for everything, it's important to me for mod to create a world that ponies live in alongside other creatures who have the same level of care lavished on them, rather than a world where ponies are obviously the chosen kind, it's a verisimilitude issue for me(yes, I know, I know). I'll change the spacings for the castes and add notes for how to remove them.
Cleaning apples should work fine, just remember that you only get one basket per ent. Since basket cleaning takes so damn long because of the body part cluttering issue I've decided to increase the yield from 5 to 8. One issue you may be having is that the baskets are rotting or not stockpiled, I'm going to see if I can get that solved. Ponies drag the ents at pony speed, travel time doesn't seem to be held up by their speed or size, but it's always an idea to have shearable and milkable animals penned in because of the Pen/Pasture Large Animal spam that no labour permission will stop, you need a wall for that.
Apples are edible raw, they can also be cooked, brewed, "sliced" into leaves like quarry bushes, made into apple sauce and conjured. Must get that graph done.
No tag to turn the ponies into vegetablists, as far as I know, only carnivore and bonecarn affect diet. Although, in the entity file there are tags for workshop and job permissions, you could just remove the ones for the butcher's shop. That'd interfere with getting ent wood, though, and various products from banana, plantain and ensete ents that are coming in the update. Plus you won't be able to process cake, chocolate, booze gum or marshmallow ponies, if you enable them.
Sprites aren't my forte, but from what me and adecoy95 were able to discern, you can only make sprites for job titles, for example, we planned to have Pinkie Pie as the sprite for cooks and drunks. That would mean ponies would tend to have the right icon for their skill rates, but that's an imperfect solution since immigrants and players will disregard skill rates for various good reasons. There's certainly no way to make it match their descriptions, even if you were willing to make thousands of sprites to match every variety of coat, mane and wing colour on an ibis zebra. Transparency is supposed to be achieved by the program ignoring the screaming pink colour.
