On the server I run I have several different worlds of which only one is loaded at a time, I store all the worlds in a "worlds" subdirectory of the minecraft server folder to keep things organized and use a script to stop the server, update the level-name line in server.properties, and start the server again.

I'm investigating migrating to Spigot from the vanilla server but I ran into this problem: when Spigot migrates the world to separate folders the migrator and the server use different locations: the migrator uses worlds/NAME_nether and the server then attempts to load worlds/worlds/NAME_nether. I imagine that the migrator is correct and the server should be fixed but idk.

Steps to reproduce (assumes knowledge of UNIX/linux command line):

1. Download a fresh server.jar from Mojang
2. Build a new spigot.jar from BuildTools.jar
3. Accept the EULA: `echo "eula=true" > eula.txt`
4. Start the server: `java -jar server.jar nogui` 
5. Go into creative and go into the Nether and place some blocks
6. Go back into the overworld and stop the server
7. Run `mkdir worlds && mv world worlds/`
8. Edit server.properties to set level-name=worlds/world
9. Run `java -jar spigot.jar nogui` to migrate the world
10. Log back into the server and go back to the nether
11. It's not the same nether! The game has generated a new nether
12. (I assume the same applies to the End, but I didn't check)

After inspecting the tree structure of the worlds/ folder, I found that the original nether dimension was migrated to worlds/world_nether while the game created a new nether dimension in worlds/worlds/world_nether.