I am finishing my master's degree this summer and one way I approached it was annotating everything I read. I used hypothes.is to annotate all of my online college readings; anything else, I'd highlight, note, and export into Notion. Hypothes.is also exports as markdown, and has tagging. I've tried to keep some order to my tags. As I progressed, it became less about annotating specific lines or words, and instead writing Page Notes, that summarized the reading.