This is a pretty open question. I like to organise by topics, most tutorials I see organise folders by file type.
I'll often have a folder for each of my primary nodes, and within them folders for sub nodes and so on. But it's a loose rule and I'll have additional folders for general topics like for example "generics" which would contain some generic classes I use a lot.
Or a "pathfinding" folder, if I've got complicated pathfinding. Maybe something like "characters" or "enemies" to hold everything related to characters and enemies and so on.
It doesn't really matter how you structure your projects directories, I just think this is the easiest way to find stuff.