Use the course as the top level, not the file type. Put lecture slides, readings, notes, and practice materials beside the class they support. This mirrors how you remember the work: by subject, week, and question, not by whether the source happened to be a PDF or a PowerPoint.
Name for the next action
“Week 05 — Trees and graphs” tells you where a file belongs. “Review traversal examples” tells you what to do with it. Keep both when you save a material. A useful name answers either “what is this?” or “why did I save it?” before you open it.
Make the source easy to revisit
Highlights and short notes should point back to the page or paragraph that prompted them. Keep notes short enough to scan, but specific enough that your future self does not have to reread the entire document.
Build a review shelf
At the end of a lecture, mark the two or three materials you will use next. A small review shelf is better than a giant archive because it tells you where to begin when you return. Organization is successful when it shortens the distance between “I should study” and the first useful action.