Create the ebook with the -X option, to stop it adding the "extra field" to the zip (the first error message), and '-Z store' to avoid compressing the mimetype file.
The mimetype file should have length 20 bytes. Check with command 'ls -l'.
If the length is greater, you probably have a newline at the end. But most editors put this on automatically. To make a mimetype file,
echo -n "application/epub+zip" > mimetype
Then create the book like this (change names where appropriate)
zip -Z store -Xr MyBook.epub mimetype
zip -r MyBook.epub META-INF/
zip -r MyBook.epub Content/
Cheers!
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