The tree is complex and hard to edit and time-consuming and not user-friendly. Would it be possible to get a button and/or keybind that says "Edit the configs such that the current ordering of items in this inventory is how these items should be ordered relative to each other"? Perhaps that would also trigger stack-combining (so 2 partial stacks of dirt would combine to the slot where the first dirt is, and the next slot if there's overflow)?

As an example, positing a Minecraft modset that removes all but these ten items (which have the default ordering as follows):
Smooth stone
Cobblestone
Dirt
Grass
Log
Plank
Stick
Iron ore
Iron ingot
Iron block

Hitting this suggested button on a chest containing Grass,Dirt,Cobble,Plank would assert that grass comes before dirt before cobble before planks, without changing other ordering, so the global ordering would become
Smooth stone
Grass
Dirt
Cobble
Log
Plank
Stick
Iron ore
Iron ingot
Iron block

note, log before plank is preserved