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@the people suggesting this function remove only calibre managed files: That can be done by just selecting all the books and pressing delete. The purpose of this function is to completely wipe the folder. This is useful when you build up junk files in the folder, perhaps because calibre lost track of some files, for example because of case sensitivity issues, or because you did not initially realize that you should not mess around with the files in this folder.
All in all, I guess I'm pretty happy with the improved warning dialog. One of my design goals in calibre is to make it as powerful as possible while keeping the basic features easy to use. Powerful tools can be dangerous if used carelessly. Using multiple libraries is not a feature a casual calibre user is likely to encounter, hidden as it is behind the calibre icon on the toolbar. I'm willing to live with the occasional user that does discover it and then fails to heed the delete warning.
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