This was interesting as I face a lot of issues maintaining my own notes accumulated over the past 15 or so years. The approach discussed might work great for the OP, but I'm skeptical this would work for me. I've found a lot of value in the "boring" maintenance tasks. Thinking about where to place something has caused me to make exactly the sort of connections the OP wrote about wanting to find. I work with a combination of a directory hierarchy, text search, and links (symlinks, URLs, bibliographic citations) which serve the same purpose as the tags and links the OP discussed. Links are how I express a lot of connections, in fact. So I don't see the organizing as some sort of non-core operation that's "labor" and not "thinking". For me, it's both.