It would be highly convenient, for those of us using larger lists of mods that all add a billion items, to have some sort of option to dump a file of itemnames that aren't in the tree, so they can be added manually. Even better if they were pre-sorted by creative tab, but that might be a bit much.

Keep an eye on mezz/JustEnoughItems#1383 and #566 for help with that. If you enable the tree paths to be in the tool tip, you can use JEI to search for /_unsorted/ for the list of items not in the tree. I am also building a better tree for modded items.