The file system works and is a common denominator. Even if you could come up with a better scheme for organizing software projects, what use would it be if no tools except for your own supports it? Using ls for listing modules/classes in a project is useful, as is removing such items with rm. So is grepping, or using some other editor than your preferred one to interact with the project. Maybe something better will show up in the future - like asking ChatGPT where your stuff is - but I'm skeptical.