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I know that Puppy can be upgraded by simply replacing the .sfs files on the boot media. Is it just the same for Grafpup?
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Yes, that is the case. You just need to replace grafpu_005.sfs with graf_200.sfs, and also swap out initrd.gz.
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I have modified a couple of system files, namely probedisk/probepart so how are they handled in an upgrade situation?
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If the files exist on both the live cd and inside your save file, the script will check the timestamps to see which is newer. More than likely they will get purged, but you do get the chance to put them back because any purged files go into a folder in /tmp. In the case of probedisk and probepart they have both been upgraded to Dougal's latest versions anyway. I also upgraded the installer, too.
Sorry about your username being snatched up, but it's good to see you here now anyway.
Nathan