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Page numbers and table of contents are very important for finding the info again. Also, they don't have to, and shouldn't, interfere with note-making. I number the pages before I start using a new notebook, and add things to the ToC at the end of the day when I do a quick review, when I also make out tomorrow's to-do list.

Numbering pages ahead of time sounds like a good way to avoid time-of-writing overhead.

I write down a LOT of my thoughts as I work - most of it I never refer back to again after that day. I like to use book darts (maybe two or three per notebook) to mark things I do refer back to more often. http://www.bookdarts.com/

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