All worlds are currently still on there, the nethers are still there, temporarily for a while, to allow admins to move some peoples stuff from one to another, Without having to use mcedit to transfer stuff. As for nethergate targets, all normal type worlds target the new nether and all nethers target the new main world.
skylands now uses the normal type environment as the skylands one no longer works(it was replaced by the end generator.), it's always had hostile mobs except they usually didn't spawn as it was always daytime in that world. The new main world is a hostile mobs type world.
You can target specific worlds now with nethergates, using certain material type in the upper corners of the nethergate.
here's the list of material types to target specific worlds.
worldv2: stone
worldv2_nether: netherrack
world: wool
world_nether: glowstone
cartsworld: mossy cobblestone
cartsworld_nether: soulsand
skylands: glass
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