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Eliminate the growth effect of bonemeal on trees. It would require more land to have a tree farm. When you plant a large tree farm you eliminate the need for bonemeal anyway. The probability of one sapling growing each second approaches 1.

I think you would have to reduce the drop rate of saplings as well so it averages 1 per 10 trees or something or you could just go out for 20 mins and grind saplings from leaves fairly easily. So it might take a few in game days to grow but you could grow hundreds of trees fairly easily.

Why not just keep track of all trees? If you destroy a tree, its carbon go back into the atmosphere. Just like normal trees; life doesn’t differentiate between planted or ‘natural’.