Then provide a GUI to modify that database. You could add a bunch of constraints in the database too to ensure the config is correct.
Usually when there is plain-text files though, it's because they want it that way. It's easier to edit a text file sometimes than rows in a database. Cut/copy/paste/duplicate files and text. Simple textual version control.
What I was trying to do is get you to explain what you mean by this:
> If our code ran in real-time to show us a representation of the final configuration, and we could trace how each final configuration value was generated, then it wouldn't be a problem. [...] But no systems are designed with this capability, even though it is quite trivial to do. Configuration is always an after-thought.
If you use conditionals and loops to create config, and then view the final json, it quickly becomes annoying when you know the thing you want to change in the final json, but have to trace backwards through the code to figure out where to change it.
So programmatic configs only work if you have this "value tracing" capability. Which nothing really does.