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ikacer comments on A Workflow with Spaced Repetition - Less Wrong Discussion
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My method is to have specific decks for when I'm first learning something, and more general decks for things I've learned a while ago.
My specific decks are for things I am currently working on. These may be for courses I am taking or textbooks I am reading. Examples are 'control systems', 'thermodynamics', or 'nuclear reactor theory'. Having them separate like this allows me to cram if needed, such as before a test. Also, if I fall behind I can catch up by studying these decks first.
I have more general decks for things I've completed learning. For example, I might move my three above example decks into a more general 'engineering' deck once I've finished those courses. This allows me to keep my number of decks low, and mixes up the cards pretty well.
I would add that it's good to keep tags if you merge decks into the main deck. That way you can always go back and selecting all cards to move them out to cram should the need arise.