There are several options described here: https://github.com/CommunitySolidServer/tutorials/blob/main/custom-configurations.md

In general, I would recommend to never replace any of the imported configurations, but only replace the components that you want to change. The override options described in the above guide can be used for that. This way you don't have to worry about copying things over. What exactly to override depends on what you want to do.

E.g., you can override the urn:solid-server-app-setup:default:CliExtractor to remove some of the options if you don't want them. Adding options can even be done without using an override.