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Correct me if I'm wrong, but isn't the main difference between flightcrew-cli and flightcrew-plugin the fact that the latter takes a directory as an argument, and the former takes an epub?
If that's the case (and I can verify that a newly built filghtcrew-plugin can handle the contents of this problematic epub) wouldn't that suggest the problem lies somewhere in flightcrew-cli's unzip-to-tmp routines?
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