I formalize comments and keep them themselves as data. I don't use JSON for this, but it'd work out as a perfect solution here. There's also good reasons to do it this way. For instance the formalized comments can work as a tool tip for a user configuration UI. Another reason is to do something like automatically produce source code from the config file with the comments in a format such that they work with intellisense. The produced source code now also can trivially reproduce a config file with appropriate defaults. Lots of perks.