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Funny how the directory structure bugs almost every new user of Calibre.
For me it kept me from really "USING" Calibre as more than a conversion program.
Once you buy into the idea that Calibre is primarily a database that contains ebooks as part of it's record and that the directory structure is the database itself it becomes easier to ignore that directory entirely.
I tend to complete the quality checking and corrections of the books, title, author name, tags etc and then use modify epub to write the new metadata into the epub. To read the books I then do a save to disk to a library location (double checking the directories of dual author titles) and organize that directory to be copied to a micro sd to use on my tablet.
By doing this I can indulge my ocd about the library while leaving the "database" alone. As for it taking more disk space, well I just picked up a new 4TB usb drive for 160.00 cdn and you really need a backup or three of an important library to be safe.
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