Keep Nether and End worlds when switching from vanilla server to Spigot, Paper, etc.

The Minecraft vanilla server software (provided by Mojang) stores secondary worlds differently than Spigot and some other third party server software. If you're switching from the vanilla server software to these, and you want to keep using the existing nether and end worlds you will need to do the following.

Note that PaperMC server software handles this automatically, so if you're using a Paper jar, nothing needs to be done. 

1.) Stop your Minecraft server.

2.) Connect to FTP using an FTP client of your choice.

3.) Look for the directory/folder for your world, the default name is "world" unless you've manually changed it. Go inside the directory, in the default case, "/world".

4.) The world directory for a vanilla server will have two folder inside of it, one called "DIM-1" (/world/DIM-1) and DIM1 (/world/DIM1). The nether world is DIM-1, the end world is DIM1.

5.) Move those DIM-1 and DIM1 directories to the main server directory (/) by dragging and dropping them in your FTP client to the ... at the top of the directory listing, this will put them in the directory higher up (/).

6.) Once they are in the main server directory, like /DIM-1 and /DIM1 instead of /world/DIM-1, rename the DIM-1 folder to "world_nether" and rename DIM1 to "world_the_end", this way your main server directory should have "/world", "/world_nether" and "/world_the_end" directories now.

Switch your server jar to Spigot, Paper, or your own jar file and start the server. It will be using those worlds now properly.

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