I know some systems leverage the modern file meta data (extended attributes), but it's clearly not successful enough that folks can use them for an application like this.

Ostensibly, things like MacOS Spotlight can bring real utility and value to the file system, and extended attributes through the sidecar indexing, etc. But Spotlight is infamous for its unreliability.

The other issue with file systems is simply that the user (potentially) has "direct access" to them, in that they can readily move files in and up and around whimsically. The "structure" is laid bare for them to potentially interfere with, or, such as the case with the extended attributes, drag a file to a USB fob, and then copy it back -- inadvertently removing those attributes.

And thats how we end up with everything being stuffed into a SQLite DB.