I'll make only a small comment here. I've used Emacs/Org for classes that I take at University of Hawai`i (they have a wonderful program to allow us old people to attend class for free). I do one directory per class and one org-mode file per class inside that directory, where attachments (papers, research, class materials etc.) also go. In math classes since homework is done in LaTeX, I have one LaTeX file per assignment. (I could do this in the org-mode file itself with LaTeX export, but I find it easier to use separate homework files. Or maybe I am too lazy to set up LaTeX properly in the org-mode file, which would be best to do.)
To-do, deadlines, etc., stay in the org-mode file which gets incorporated into my agenda. Although managing multiple attachment files is necessary I find that the closer I can get to one file per project (whether a class, a novel, an analysis, etc.) the more efficient I can be. Bob Newell Honolulu, Hawai`i
