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where i put *.patch files?
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The patch files go into the .autopatch folder. You can have several of them, as described in the first post. E.g. libnickel.so.1.0.0-something.patch and libnickel.so.1.0.0-other.patch. In theory you could give each independent patch its own file and just move the ones you don't want to disabled/.
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If i put *.patch in disable/ the program disable the patch independent of the yes/no switch?
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Yes, it will act as if the patch wasn't even there. You could just as well delete a patch file you don't want - but moving it instead gives you the ability to move it back at a later time.
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When the patch is applied the files remain in the same directory or it is move to avoid be repatched the next time?
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Repatching is avoided by remembering the input and result of the last patch run. If you modify any of the patch files, they will be reapplied.
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Edit: Is there some date to the next beta?
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Right now I have a slight motivation problem with this mod; 1) there seems to be little interest/feedback, i.e. people seem to be happy patching externally as it were; 2) while I did a lot of patching on my last reader, I find I need considerably less patching than expected on the Kobo after all.
So right now I'm not sure if / when I'll find the time / motivation to make a new beta.