During the rewrite in 89e55e9065, a queue system was added to allow
using both VoxelManip-based generation steps, and set_node-based steps,
however some set_node-based steps (underground mushrooms, nether
decorations, and structures) were missed and remained in a VoxelManip
step. The result is that the changes made by the set_node stages were
overwritten after the (now-stale) VoxelManip data was committed later.
(ref. Mineclonia/Mineclonia#26)