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@JSWolf: I thought you must have known the answer to this. You have stated that people should use calibre to delete books as it does the cleanup, so I assumed you must have know what was left behind.
@compurandom: The covers are cleaned up properly when you delete a book through the UI. The Kobo Utilities cleanup was written at a time when there was problem with this. And because I needed to prove what was actually happening.
But, nothing is left behind when you remove a purchased book. For sideloaded books it depends on the format. For anything that is opened using the RMSDK (epubs and PDF, don't know about other formats) there will be files in the "Digital Editions" directory. For everything else, if the last book or cover in a directory is removed, the empty directory is not removed.
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