Turns out Bukkit YML is easy. I've replaced NUKE_WORLDS with a conventional config.yml. We'll auto-create it on plugin startup.

You now use a list of files and directories for the nuke option, like this:

nuke:
 - world
 - world_the_end

We delete files, directories, and JSON files get cleared not deleted.

You also get a setting to turn on the per-snowball logging, which is off by default.