Don't know how you found it but want to share automatic tool. Go in godot to Project>Tools>Orphan Resource Explorer
And you can also add .gdignore to the folder if you know there aren't files that should be accesed by godot
I can also give you one more recommendation about further optimization of godot. Compiling it from source with disabling unnecessary to your project features although it is a bit not flexible tool to cut unneeded thing or even use build_profiles which are a raw/experimental piece of ***** but work greatly