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In Fedora 5 and earlier, RDF resources as well as small (sub 10K) binary files were stored directly in the database rather than being written to disk. This was a performance optimization in Modeshape (Fedora 4 and Fedora 5's storage layer) that came at the cost of having an obscure representation of repository data. So Some resources were stored in a database, while others lived on disk. The user and developer community found this approach unsettling especially when trying to troubleshoot issues. It required intimate familiarity with both the bespoke database structure of Modeshape as well as its application logic for where and when to store repository objects.
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