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I can create zip with winzip, but winzip needs to be installed to work on the user's pc. I don't want that.
I found pkzip25, which also can create the required type of zip file, but not with files already compressed - like KoboRoot.tgz is. If I try to compress a text file for example, it will create a Kobo-compatible zip. Kobo will extract the contents to .kobo. But if I try to compress KoboRoot.tgz with the same settings, it creates a zip with "store only" method. That is very frustrating at the moment.
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