I find this particular problem really annoying, so here's what I want to be done about it:
Let's say I have 10 Lion Skulls buried, and only want to dig up one. There is only the option to dig up the whole stack.
So, I thought, why don't the mods add something like this: a little thing on the item stack you want to dig up. A text box. It could be like:
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"DIG UP STACK or DIG UP: (text box)"
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That way, you could input how many you want instead of having to dig up all of the items in the stack.
I'm aware that you can manage this in the Organisation tab, but it’s just a small tweak that I think could save some time.
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Feedback is appreciated.