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I think for those who don't want any software to touch their files and folders, an independent tagging program would do it. I used to use TaggedFrog in Windows. Now, in Ubuntu, I still haven't arranged for this, but I found a java program called SCAN at sourceforge.net can do the trick cleanly.
And by the way, Worldwalker's great explanation of calibre should somehow be included on calibre website, so noobs like me don't just play with calibre for 5 minutes and then uninstall it.
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