The Zettelkasten note-taking method has made book writing and writing scientific papers easy for hundreds of years already.
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Having just read this, after rrieke's post, and having also just started to use UIDs, including adding them to old notes, I'm thinking it might be a good idea, before I go any further, to go ahead and prepend a UID to every note's filename, based on the date created (or possibly modified). That might preserve some of the "date memory" chunking that can be so useful.
I'd add them as you go. Think of the ID as a socket. The magic happens when the plug goes in the socket (no pun intended, for now): When you link notes together in a meaningful way.
Good advice; thanks.
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