The purpose of those folders is to implement Lyra, which is a framework that makes it easy for you to build your game as one or more GameFeaturePlugins.
Think of Lyra like the Engine. You don’t go putting your code in the Engine source area right? Same with Lyra. Don’t put your code in the Lyra source area. Instead, you make a GFP and put your source there.
There are rare circumstances where you must make a non-GFP plugin to contain some code (for example if you want to modify World Settings). But in general you can do most things in one or more GFPs.