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Microsoft originally faced a similar problem with their Sharepoint product. Early versions of the Sharepoint Team Services product kept all documents, calendars, etc in user files.
Eventually they moved it all into a SQL Server database. It might seem counter-intuitive to put all the eBook content into a SQL database, but Microsoft realized two advantages: with everything in the SQL DB it becomes a "black box" which no one attempts to monkey with (an oft avowed objective stated here by Kovid and others as to why file structure will not be changed) -- put it all in SQL and the requests for file system structure requests will go away. Microsoft also did a lot of tuning so performance with docs in a DB is far superior to when they used the file-system. Don't know but whether there might be some synergies possible if both metadata and eBook content are maintained in a SQL DB.
Just a thought...;-)
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