I've been working on a tag-centric document manager for the last 90 days: https://getpolarized.io/ It allows you to tag and manage everything you're reading and the primary management metaphor is the 'tag'. It's a central repository for all your reading. PDFs, web content, and it supports annotation (highlights, comments, etc). There are a bunch of clear wins here. Related tags are awesome. You can build a bunch of r…
You're at the mercy of a search engine's implementation and index foibles for finding things through search queries.
A hierarchy maps onto our spatial memory, which we use to figure out where we've been and go back to it.
There's a lot to be said for maintaining spatial metaphors in information space.
Another little detail here is that spatial organisation (in meatspace) is a shared environment. A single 'shared' ontology is useful even if it's nonsense, because it's still a shared frame of reference in which navigational directions can be shared.