Thats really common in C++ Development :D
you can find the "real" code in the godot-repo on GitHub. https://github.com/godotengine
You can use the headers for example to build bindings.
And the bindings + Headers are used to compile Gd-native-Librarys. Those Library don't have any life in it, until you throw them into the Engine.
But the main implementations of the hot stuff are always in the Codebase of the engine
I can recommend you to take a look at my Godot C++ Steam Guide. This will help you out to understand the possibilitys :D