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phossler - darn, I didn't think of a VBS script
I don't hold with the 'it's a black box/crinoline so you shouldn't opening/look-under it' point of view, its your data, on your computer, thus you're responsible for it. There are no warranties to invalidate here.
When the Library Check function throws up an error often the only way to fix the error is to open the library/author/book folder and deal with the file/folder in question (delete it, rename it, add it to the book...). Blithely having calibre delete it (when that's possible) could result is removing something whose loss you later regret.
My position is 'look but be careful what you touch'. Where 'touch' is to add, delete, rename or alter the disposition (attributes, permissions, etc) of any existing folders or files. If Kovid didn't expect you to you look then he wouldn't provide the press 'O' or Click to open features to open a book folder. And he'd super-hide the library folder in some obscure location with an obscure name - a' la Picasa or some such
BR