In my experience this can be a nightmare! What I do now is that I have a clear distinction between build types. First is prototyping, then production.
Prototyping is where you are now, with tons of additional files, test scenes, assets all over the place, probably additional scripts hanging around and basically a big plate of spaghetti. That is brilliant though, you have been trialling, learning, developing, exploring, changing things, this is what prototyping is all about.
Then comes the production build. It can seem more boring than the prototyping stage but it has it’s own sort of elegance and challenges. This is where you are creating the version you are going to share or sell. The clean one. What you are essentially doing is re-creating your own game from scratch, but this time, your only focus is on clean and maintainable code and structures. Nothing should be brute copied from the original. Every script should be checked and re-factored, every asset stored in your now perfect folder structure and only if needed. Creating this beauty of a version does not take as long as it sounds like it might, but it does take time, it is not a job completed in a day (at least usually). You are not adding anything now. Get a good idea suddenly, too late. That was for prototyping, not production.
The decision to move into production stage is a big one. You are happy with your game and it is feature complete. Now you can start building the clean version.
So cleaning up a project folder is no longer a problem. You don’t have to any more. Because this is not your production version.
Think about it like this. When a new machine is invented it is created in a workshop, probably with bits all over the place, oil on the floor, early versions sitting in corners, failed versions lying around in heaps, scrap piles, useful bits here, bits that need further exploration over there etc. But now the prototype machine is built! It works and does the job it was intended to do perfectly. Now do you just clean up your workshop and start production, or do you go and find new premises, set up a production line, get your staff trained, get all the bits you need in order and tidy. Prototyping is not production, and production is not prototyping. Prototyping is messy, fast coding to try stuff out, dirty loops and crude data structures etc. Production is clean, reliable, tested, safe and free from clutter (and maintainable). Production is pure.
So when you are ready, don’t bother wasting time ‘cleaning up a prototyping folder’, just start a new project and build your production version from scratch.
Hope that helps.