I'm reading "The Science of Managing Our Digital Stuff (MIT Press)". They seem to prefer hierarchies (I'm not far through the book yet).
We might not be able to get away from hierarchies, if experience with "memory palaces"  gives an indication of how most of us remember (would be interesting if we could identify the memory palace equivalents for those who remember using auditory, visual, and tactile forms ). Most memory palaces' dendritic structure bears a striking resemblance to a hierarchical system.
I still find an overall hierarchical structure, combined with indexing and tagging, as the most flexible system with today's technology. I'm looking for ways to implement automated tagging using auto-summarization, voice commands, and automatic environment-contextual cue gathering, and expanding the indexing power with automated ontology extraction. Primitive example: I pick up an incoming call from a client, the system automatically transcribes the conversation, identifies the client, files the recording and transcription to a project folder, analyzes the content of the discussion, and auto-links relevant emails, chats and documents with bi-directional hyperlinks based upon concepts vocalized and conceptual relationship maps extracted based upon a crude initial morphological analysis of the conversation. The accuracy doesn't need to be astounding for this to have use to me; just a crude approximation is sufficient for me to start with.
Thoughts on Camlistore: I agree with their high-level https://camlistore.org/doc/principles and https://camlistore.org/doc/uses . Their presentation slides and videos gave a helpful explanation and demonstration of their functionality. The query string format and showing of live search results were very cool. I have doubts about the rich JSON metadata format, their model of mutable files, and whether I can represent and query the my kind of metadata in their system.
Thoughts on "Science of Managing Our Digital Stuff": I sat down at the public library and read part of the book. Your early warning about hierarchies proved correct. The authors seem to be very focused on conducting user studies and timing people's time and recall performance. All their text point toward the superiority of hierarchical organization due to the efficiency of human spatial navigation / folder traversal. The book has some interesting perspectives to offer (e.g. human behavior, group information management, motivations behind keeping data), but I don't expect it to contribute to any of my technical design decisions.