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The reason it isn't that way in the instructions is precisely for the problem pointed out by Dopedangel. It is very important that you delete the original calibre folder before replacing it. If you forget to do that, it can cause problems. Whereas, if you forget to do that with the calibre libray and/or calibre settings folders it wont cause a problem. Therefore, in the interests of robustness, the instructions are the way they are.
Someday I will get around to wrapping that zip file in a simple EXE that does the replacing for you after you tell it where to put the install.
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