Not made for storing 'all the facts [of our] lives' - but an interesting example of a robust physical system for knowledge organization is Niklas Luhman's Zettelkasten Method[1].

It translates well to a digital medium. The general idea is a collection of granular information (notes) interconnected in a non-hierarchical way using tags.

[1] https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...