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Originally Posted by capnm
I noticed those too, as ones I'd happily lose without a second glance, while most of the other unmanifested files I'd tread more carefully around.
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Ok, I think I see where you and drMerry are going with this. There are files that you would "quite happily lose regardless of whether they are manifested or not", and "the rest".
Calibre bookmarks I think has to remain separately treated as there are users who do read their books in the calibre viewer and want to retain their last read position etc. So while many users would quite happily lose them, there are a number who would not.
iTunesArtwork remains a question mark. Like I said in a query I ran across around 18000 ePubs I didn't have a single one where the iTunesArtwork was manifested. So my natural instinct is to nuke them but as drMerry has found one situation I remain open to hear anything more concrete on that.
That leaves the iTunes plist files, .DS_Store and thumbs.db files which are all just "trash". As drMerry points out they may have been included in your manifest by a user running a tool incorrectly on them or through ignorance.
So perhaps the "Remove iTunes plist files" option is renamed to something like "Remove unneeded junk files" or some better name. So that way a user can always leave it turned on if they so choose and not have to tick three checkboxes. Potentially iTunesArtwork goes into that category one day too, and Calibre bookmarks remains separate.
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Would it be reasonable to stash the filenames in a tag-style custom column?
Then we could easily decide how to deal with various files as we discover them ...
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This was why I added the log capability to the latest version of Quality Check. Copy the log results to Notepad++ or wherever, then run Modify ePub appropriately on the books shown ticking only what you feel safe to on each book.