I think this is a great example of the old saying "You can please all of the people some of the time, and some of the people all of the time. But you can't please all of the people all of the time." Kovid and all the other contributors to Calibre work very hard to make Calibre as useful and "pleasing" to as many people as possible. And they do a great job of it. But there is no way of pleasing everyone. If Calibre deleted to the recycle bin, it would, as Kovid pointed out, a) take forever and b) possibly fill up someone's recycle bin. This would "displease" a great number of people. Instead, they rightfully make the choices that will "please" the greatest number of people, including, as in this case, doing exactly what is promised--deleting the files permanently. And should a bug or other legitimate problem be posted, they do their best to resolve the problem, usually by the next weekly release. And all of this is for free. Even programs that are paid for don't often provide that level of service.
@kovid--I think the only way to make the confirmation dialog clearer would be to use bold and all caps on the "permanently deleted." But no matter what you do, the user has to actually READ the message, not just auto-click on it.And there's no way to ensure that.
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