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Description of your suggestion.

I've been chewing on the fact that base game minecraft water bottles are classified as potions and the croptopia water bottles are required as a work around for that. I entirely understand the need for this-- java classes and class logic can be a time, and the game isn't really set up to accommodate juice and the other cool stuff this mod adds. I think the main problem is one part resources, one part immersion in my experience. Yes, croptopia water bottles are harder to reuse than water buckets, and this is frustrating (and already something that you're addressing!)-- but more than that, croptopia water bottles exist in the world with pretty much no in-game universe explanation. And this may be silly, but... you also can't drink from them, or from the milk bottles, so it's like having this strangle, inexplicable brick in your inventory that you can only craft with and that creates an entirely different type of water bottle (the vanilla base game bottle) once you consume what you have crafted.

Suggestions for QOL and immersion:

1. Let players drink from croptopia water bottles and milk bottles, just because it's a thing you can do to make the item feel more interactable and less like a weird inventory brick. Maybe make it so that drinking milk bottles has the same effect as drinking from a bucket? I personally don't think it's super game breaking to have a stack of milk bottles that you can do that with, since they're a little more difficult to make than your standard milk bucket due to the extra steps!
   *However, if you disagree because of design choices and say, nah, I think that's pretty game breaking, then how about a tradeoff? You could create an extra step for milk bottles that you can drink from--essentially pasturization. Boil the milk bottles or cook them on a heat source, which takes time, and boom! You've got a portable, stackable cure for bad omens!

2. In that regard, how about making something like a water filter? I know, adding another tool might frustrate some people, but it could justify the presence of the fancy croptopia bottles and the difference between the vanilla bottles and the croptopia bottles for immersion reasons. Instead of the name being Water Bottle, the same name as the vanilla bottle, it could be Filtered Water or Drinking Water, Potable Water, etc. I know that in real life, charcoal can be used to purify water to an extent--maybe that could be a component of the water filter? I know Brita water filters use activated charcoal or w/e. Alternatively, I guess you could have people boil it. Up to you if you decide that this makes sense! The water could heal some hearts (probably not many), unlike base game vanilla water bottles, and then boom! People are possibly less frustrated by it!

3. Maybe let people make croptopia water bottles from vanilla glass bottles + water buckets so that there's a way to reverse/convert them back! It could be a one to one for the bottles. Just make sure that people get their bucket back y'know?

These are all just suggestions-- I support whatever direction you end up taking your work in. Thank you again for the mod! I'm having a lot of fun with making apple pies and cranberry juice!