I feel this was not accepted well on HN because of lack of context. The author isn't trying to "solve the web" or propose a better solution for general file system. He's describing a solution to organize his note-taking system, nothing more, nothing less. Most of criticism here don't apply to this use-case.

I thought the article made a lot of sense in that context, having also struggled in past with organizing notes: nested folders vs flat structure, longer 'document' notes vs short blocks, tagging, inter-linking, discoverability...