Microsoft Sharepoint uses SQL Server for all user Item storage, so it's an example of an all relational file store. They did this around the time they were also experimenting with the Cairo a sibling comment mentions. Also as another commenter noted you query on the metadata. Folders/directories for instance are represented as metadata. Installations can also describe very detailed ontologies including ones provided by third parties. It's a lot of work.

Edit: I think I was actually thinking of WinFS which came out of Cairo later, around 2000.