Null pointer error in server tick at start of game

• • UPDATE: See additional information below. Actual bug is: Structures do not regenerate correctly when chunks are regenerated. Null pointer error actually happened on a world that originally had forge, and was re-loaded into vanilla; and did not happen on a world that was a re-creation in pure vanilla.

—

Well, it crashed in startup.

What I did: I am trying to track down the source of "ghost towns", generating with no people, no chest in the smithy.

I have managed to reproduce this with forge, only – no mods. So now I needed to see if this happened in vanilla.

I found a town. Quit the game. Deleted the region files, so that the world would be regenerated when I logged back in.

What I expected to happen was...:
The world would be created, either with a village, with people (in which case the problem is with forge), or without people (in which case the problem is with vanilla).

What actually happened was...:
Null pointer.

Steps to Reproduce:
1. New world.
2. Find a village.
3. Quit game.
4. Delete all the .mca files in the region folder.
5. Restart.