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I have been using a ~/notes folder with markdown files edited with vim on my computer and markor on my phone synced with syncthing. That works well. But I am also a fan of paper notes and find that they "stick" better in my memory, and I am more conservative and intentional with what I physically write. However I end up with an out of sync feeling - some information stored digitally, some in a notebook. I've been considering strategies to address this.
One strategy I thought of is to use a single markdown file like the Hamster system [1] and alphabetize the sections; then I print this file and take handwritten notes onto the print out; then when the diff is large enough, I update the markdown file, print it again, and repeat. The main disadvantage is needing to reprint the full file for what could be small changes. To address that I have considered putting a page return between each letter of the alphabet, so each section starts on a new page.
Do you have any strategies to effectively synchronise paper with digital notes?
[1] https://github.com/slowernews/hamster-system