I've been struggling with this as well, and re-organize my directories every year or two, or when its starting to get out of hand.
The best solution I came up with was to first put every project in a repository - this way, you can track changes, and add documentation where required. On my local machine, I also split projects by where the repositories are hosted (github, bitbucket, etc..) so that I can use a .gitconfig file to control what credentials are being used when a project is open in my text editor and / or IDE.
I also delete local copies of my code when I'm not using them any more, just to reduce the clutter and free up some mental load.
However, you'll still face the issue of having to give a unique name for each of your projects - one of the hardest things to do in our field 😂😂
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