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Forget about folders. Use a good metadata schema.
Feel free to elaborate. ;) I don't mind ditching folders. The question is: how do I get at said metadata with the least amount of manual effort, how do I make sure that it's accurate (sifting through thousands of files is not fun), and how is the metadata stored - particularly so that does not lock me into one application that can only understand its own metadata scheme, and once it dies or I want to switch to a different one, I lose all the work I've put into curating my collection. That's why I was considering folders as an option: they are a software-agnostic way of organising my library.