ASP.NET Core documentation suggests we should use appsettings.json file, along with a file per environment, containing overriding values. The problem is that all these files are published, though only appsettings.json and appsettings.[Environment].json are relevant. The other problem is that to change a config value on server one must inspect both files: base and environment specific.
So my question is: what is the cleanest way to have one configuration file in each deployment environment?
The key difference is that ASP.NET Core apps are not deployed for a particular configuration, as ASP.NET apps were. Previously, you'd literally publish as "Release", for example, and if you wanted to switch the deployment config, you'd have to republish. With an ASP.NET Core app, the environment is determined by the ASPNETCORE_ENVIRONMENT environment variable or by the environment passed during execution. As a result, it's perfectly valid to deploy all possible environmental settings, since the environment can be changed on a whim.
That said, if you know for sure you're never going to change the environment, you can simply remove any appsettings.{environment}.json files you don't need. Additionally, you should not really override settings in the man appsettings.json. If it's environment-specific, it should go in one of the environment-specific JSON files. Your main appsettings.json file should really only contain global settings unaffected by environment. If you handle it in this way, then you don't have to look at both to see where the settings are coming from.
Finally, if you don't like this approach, in general, you can simply choose a different configuration strategy, such as environment variables or an external config source such as Azure Key Vault.