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Basically, the KoboRoot.tgz file is part of the automated installation system. New Kobo firmware and third party modifications use that file for installations.
For example, when you use the KoboPatcher, the output file from the patcher is a KoboRoot.tgz file which gets copied into the .kobo directory in the root of the exposed partition (what you see using a USB connection) and will be automagically installed when you eject your Kobo.
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