To manually remove them if you can't automatically with Preware or WebOSQI:

sudo /var/usr/bin/patch -R -p1
-d / < /var/usr/palm/applications/org.webosinternals.patches.xxx/xxx.patch (replace xxx with patch name

Obviously this won't automatically remove any directory's, but will reverse any patches that for some reason don't show up in either Preware or WebOSQI patch categories.

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