You’d think games with crafting would have solved this issue by now, but it’s still pretty much standard to let the player deal with that mess themselves. There are tons of solutions for this issue that might not be perfect, but are certainly better than making the player spend a significant chunk of playtime sorting and/or searching inventories and chests.

ME system my beloved

I always try to organise my chests and I always end up with chests of shit I just can’t be fucked sorting

My inventory and ender chest are full of shulker boxes containing unknown items

Build an auto-sorter, so you can put it in a chest full of random junk, and it’ll output it into labelled chests.

The humble AE2 system:

i unironically always end up adding Tom’s simple storage mod to my vanilla+ modpacks, and it’s always much better than vanilla. Even better than huge unwieldy and expensive and slow storage systems that take hours or days to build. It’s one convenience I always use, because otherwise I will quickly abandon a world. What it does is add an AE2-style interface to just a bunch of chests that are next to each other, plus a few other things. You’re still storing things in chests, but it gives you a clean look at all of them at once, instead of having to dig through dozens or hundreds of them.

(my 1.21.10 world doesn’t have the mod installed yet, but I only started a few days ago and so far the amount of items is still okay. But eventually I can’t help myself, I cannot manually sort items, I’m just not built for it, and automatic sorting is excruciatingly slow, and item retrieval in big storage systems is also very slow when you need to run back and forth just to grab a few different items. Plus traditional redstone-based sorters break when you quit the game while they’re sorting.)

has shears but no leaves or wool

Kind of nice that in Necesse you can let your villagers sort chests for you.