This is an explanation on how to add your own C++ functionality to Godot by adding your classes to the engine which will also allow you to add them to your game and edit them from Godot's Editor. So for example, if you want to have change the behavior of Node3D class on Godot you can use a module to create a class that inherits from Node3D and add whatever functionality you may like...
Documentation link: https://docs.godotengine.org/en/stable/contributing/development/core_and_modules/custom_modules_in_cpp.html
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