I would suggest making notes which contain discretish ideas related to certain themes (which will be your MOCs or folders), so that as you progress through the degree you can organically expand on and easily file new stuff you learn with what you did in your first year. Then riffing off Nifty’s suggestion, you could have tags for each note which reference the course/semester you learned it in, or maybe even the week of that course/semester if you find yourself making loads of notes?
This means they will be set up for you to learn pretty fluidly, with old things you learned popping up where relevant to your current concerns, but you will also be able to easily review what you learned in sequence when studying for exams or whatever.