I too have been thinking about alternatives to hierarchial filesystems. Originally I thought that I wanted a tag based system, but currently I believe that tagging adds too much overhead and that it might not scale well either for the user since the more tags you have the harder they will be to remember and then there is the issue of relationships between tags.

On macOS they have a view that shows you all your files in the order that they were last modified. That has value I believe. Combine that with optional categorization for filtering, so tags but with the tags not being at the very center, and store files by their hash but keep filename for display. Also keeping track of origin of files - user authored vs made by others. Documents with hyperlinks are used for organizing files of current concern. Snapshots of all files are kept so you can delete, replace or update "indexes" over time but still being able to retrieve them later. Append-only except for the pointers that show what indexes are active.

Hope any of that made sense. It's a bit late and besides I didn't want to write "a whole book" in this comment.