Note: the accuracy of this specification may be flawed. This specification is believed to be correct as of beta 1.0.0.7, but its accuracy is by no means guaranteed.
The ability to set biome colours disappeared this update, which is a shame. The old method using biome IDs is back; colours and gradients are now handled automatically client side. While this is a bonus for PocketMine in the way that biome colours in Anvil worlds will now work correctly again, it's a shame to see that capability disappear.