It took over a decade, but I finally realized that this is the original purpose of the dialectical journals I was required to write for my high-school English classes, before they were coopted as an assessment tool. As it’s a record of your own thinking about the various things you’ve read, it provides a way to figure out where ideas came from in a way that full-text search can’t handle.

These days, I use a traditional index card system combined with a spaced-repetition flashcard system. Each concept that I feel like collecting information about has a small stack of cards that starts with a 1- or 2-sentence definition, in case I’m using a term slightly differently from other people. Below that are cards that represent quotes, notes, summaries, and recommended reading on that topic.

The flash card deck is to make sure I know what things exist, and what words are used in the literature to refer to abstract things. If I need more detail than I can remember, those keywords will get me to a relevant wikipedia page, at least.