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Originally Posted by Jellby
Not really. -r is, because otherwise the files in the subdirectories are not stored. But the rest just make the epub file somewhat smaller. -9 simply uses highest compression level, -D does not include entries for the directories themself, and -X does not store additional file attributes. As far as I know, neither -X nor -D are required for ePub compliance.
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I've seen epubcheck scream if you don't have some of those flags. I'm not positive about which ones, but at least one of them is definitely required. Probably not -9; it's just a good idea. I think it was the -X flag, without which, at least in OS X, you get all sorts of errors about illegal fields in the ZIP file caused by the way it preserves file permissions and EAs. I'm assuming most of the same behavior occurs in Linux.
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And "-x .DS_Store" may be required only if .DS_Store files exist (in a Mac?)
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Right. The hack to remove Finder turds is definitely not required on Linux.