Fedora 3 stores all its data as plain old files on disk; for backup, you can simply backup the objects/ and datastreams/ directories, and you'll have everything (one of the nice features of Fedora 3, that has been carried forward to Fedora 6, is the ability to rebuild your repository entirely from data on disk).
Are you considering organizing the files in a BagIt structure for preservation purposes? Are you looking for something a little more human-friendly than the Fedora 3 directory structure? FWIW, Fedora file storage is based on OCFL, which is very similar to BagIt, but with versioning included.
-- Scott
--
Scott Prater
Digital Library Architect
UW Digital Collections Center
University of Wisconsin - Madison
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