I'm having trouble figuring out how i would go about adding a custom mob into my generated structure the mob is a boss like mob so i only want it to be spawned once. Any idea on how i would do that?
Well, structure generation is just your own code that places a bunch of blocks. You can simply add any other code you want as well, including mob generation. Why not just add code to spawn the mob after the blocks are placed?
What about times when you want non-boss mobs to spawn in the structure, like how Magma Slimes and Wither Skeletons spawn only inside Nether Fortresses? How do you go about setting that up?
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