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For settings files I always have an example file with sensible values filled in and along with descriptive keys that serves as reasonable documentation. If something is truly unknowable, I’ve probably done something wrong.
How would you mark a flag in your json settings file as deprecated?
In my opinion, the settings file isn’t where this information should be presented. I would put these notes in the release log and readme and example settings file. I have also written this information to logging during startup so a user knows what to do, or I write a migration that does the change automatically if that’s possible.
This is only my opinion and you can use the comment method described like
“//“: “Deprecated”
if desired.