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Rather than reordering Calibre's files, I suggest either maintaining a backup copy (I keep a portable version on USB as a backup) or using "Save to Disk" as a mirror of all your ebooks. In the latter approach, you can arrange the ebooks any way you want, e.g. <publisher>/<author> - <title>. Under "Preferences" select "Saving books to Disk" and setup the "Save Template" to how you want the ebooks to be arranged.
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