Well, just so you know, I cleaned that bench before the photo. I'm usually working on several things at once. So it's usually fairly cluttered. My wife was just in my shop a few minutes ago and couldn't find a place to put something down. Ugh!
The sketches I don't really ever refer to again once the prototype is made. I save them but have so many after 38 years of work that I'd have to search through many hundreds in a banker box to find it. I used to organize them by job number or put them in a special sketch book but found that I so seldom go back that I could skip that. I do make any needed sketches on the job envelope.
The prototype molds I keep separate from any other molds, on a shelf with a number on the mold front and a sketch on the top. I note wax injection pressures on the mold if needed. I'd note that I did have several important molds stolen by an employee years back, so it's a good idea to keep them locked up.
The photos I store on a computer. Although I am terrible at stopping work to take the time to photograph it.
The notes for making on the envelope are things like tubing diameter and wall thickness, even how I coiled the tubing and the final inside diameter of the coil. Just so I remember how I made the components. Like that.