Basically what I'd love to have is a plugin that I could run ONCE every time the server software is updated to re-generate the "virgin" terrain just like I selected it all and used //regen with WorldEdit. By virgin I mean a chunk who was not altered, to the extent that we can possibly understand of course. The rules for detecting a virgin chunk could be basically to see if the chunk contains man-made blocks, like cobblestone (unless it's near a spawner), torches, wood, bricks and so on. The result would be to update the world with stuff introduced in the new updates (like dead shrubs in the latest one), but leave the constructed area untouched. Am I the only one who thought about this? Ah, it would NOT be a problem for me if this plugin required worldedit as dependency.
You should take a a look at WorldEdit's source - https://github.com/sk89q/worldedit/tree/master/src/main/java/com/sk89q/worldedit
That's what I've been going off of, but it's very confusing how he has it set up. There's a lot of overridden classes with the same name.
He just gets the region that is selected and regenerates it, you should do the same but "force" the region to be a full chunk