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I like your idea of the "pre install" script the best, especially if we can backup the files to somewhere on the native filesystem. I think this would be the most seamless approach.
In the long run, I think we'll have to work on finding FOSS replacements for those two programs. The keyboard will not be too hard; I think there are already some options out there. Replacing Mobipocket will be harder.
Although... Mobipocket is a Java program, right? So theoretically we could upgrade the Java stuff when we upgrade the kernel, and leave the Mobipocket binary alone, and it would still work, right? So we may never have to worry about replacing Mobipocket, just about replacing the Java underneath it.
Good catch, Adam! I hadn't thought about this problem before.
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