I also have thousands of Bristol cards. I use them for detailed notes on the books I read, and more general notes as well. I call this “the material.” It’s whatever may be useful one day. Sometimes these cards contain fragments of my future books.

But organization is key to developing a knowledge base, and in essence, that is exactly what a PhD is: developing a knowledge base that allows you to hypothesize, make inferences, extrapolate, connect. Daily notes, project notes, notes on papers, code documentation – all of it should lubricate the wheels of future thinking / work.

Flat organization: no hierarchy

Hierarchies are so 2nd millennium. Links and tags ought to be enough. This verges dangerously on relating more to my philosophy of notetaking than my technical needs, but I want a tangle, not a tree, and my tools can't force the latter on me.