I'm another academic mathematician. I'm not really convinced that all this would be a time-saver for me as far as research productivity; maybe I'm just old-fashioned but I just have a few folders for paper notes and that's it. But certainly this could vary from person to person. To me, the place for the real time savings is organizing your teaching workflow. If you're a grad student, make sure to get on top of that A…
I keep questions, slides, written notes, etc. controlled and semester-specific things in a directory that isn't tracked.