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The problems I see with the folder structures are the inconsistencies. The sort order inside the database is opposite of the folder structure on disk.
Also, if you do a Save Files to Disk, the output is also opposite of the folder structure. This complicates a backup because I back up the entire directory but I'd also like to do a File Save to Disk to get the .opf files. Of course, this creates another folder and copy of each book. I know this backup strategy is redundant as I don't need the opf files if I have the metadata.db file. I just hate having to rely on one big single file to have all my information.
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