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Fwiw, I have a particularly nasty example of the consequenses of Calibres editor not showing the file structure. The file is a merge of five books to one, using Calibres plugin to merge epubs. The files are all jumbled in the editor's browser, but opening the same file in 7zip showed that it was actually quite well structured, with each book in a separate folder. (And to be just, Sigil didn't like it either, so I ended up doing the merge "by hand" so to speak.)
Regards,
Kim
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