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1) the system on the kobo unpacked the file and distributed the contents appropriately based on how they were stored
2) yes you’ll have to do most of that work again. There’s a file in the base kobo patch folder that overrides the “no”s from the files in the src folder but I’ve never seen much use for this myself, partially because I modify some of the patches to my tastes anyway and thus need to go into those files and also because I’ve not taken the time to really learn how this file is used.
But this really isn’t the thread to talk about this in. There’s the patching instructions thread which would be more relevant and more likely to get you full answers
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