Calibre is a free, open source, incredibly useful application that many of us rely on to side load ebooks to our devices. Without it the options available to us would be severely limited.
If the creator of the application wants to change the icon and prefers the new look, I don't know how we can reasonably criticize this decision.
Also, as he previously stated, the application is open source - so if it bothers you that much you can go through the process of changing it.
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