I've always found the companion software to be next to useless, and use the Java program to merge scribbles. Mobipocket Reader isn't necessary because you can buy/download books directly from the site.
I've heard Mobipocket creator runs without a problem in Wine, but I have a Virtual Windows machine that I run it on.
Linux is great for the average person when they don't know they're using it. Unfortunately, we live in a windows world.
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