There are multiple reasons why tools shouldn't be doing this. First, I don't like tools overwriting my configuration. My dotfiles belong to me and I have thing

There are multiple reasons why tools shouldn't be doing this. First, I don't like tools overwriting my configuration. My dotfiles belong to me and I have things configured the way they are for a reason. Tools should inform me if changes are required to my configuration, and not just go and change it by itself. Second, it prevents users from making their configuration files read only. This affects users of Home Manager by the way, which deploys configuration files as symlinks to read only files under /nix/store. Even more egregious are files that write mutable state to configuration files, which makes them unsuitable for version control. Unfortunately, Docker is guilty of this and stores mutable state in config.json. Finally, as mentioned, it interferes with XDG adoption. Personally, I'm all for breaking tools that write to user configuration files. They cause too many headaches with no clear benefit.