That’s an impressive and thoughtfully structured system, especially at that scale. The use of symlinks and a separate version-controlled notes repository makes a lot of sense for long-term archival.
I’m curious — when working with such a large collection, how do you typically rediscover material or connect related ideas across different parts of the hierarchy? Do you rely primarily on directory structure, full-text search, or your notes as the main index?
And as you move toward merging the PDFs and notes into a unified system, do you see the notes becoming the central navigation layer, or will the directory structure remain primary?