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You cannot change anything about the internal way that calibre stores book information, and should not be tempted to mess with it in any way or you are likely to cause problems when the file system no longer matches the Calibre metadata database.
You should always use Calibre itself for browsing the books in the Calibre library and for getting books into and out of the library. That way you do not need to be concerned about the details of the internal storage.
If you use Calibre to export books using the "Save to Disk" facility you can set the template that is to be used for the folder/naming structure to be used for the saved files.
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