I’ve seen a few where they have a config.yml, and a plugin.yml (which no user ever touches since it’s part of the jar >_>) and then a commands.yml
home: true
fly: true
foo: false
msg: true
bar: false
and so on. After peeking under the hood, (for safety, ofc) I noticed that any value that matched null would then be set as false, and would be written to the file as such. Not a bad idea at all.