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I'm not an os x user so I cant be certain, but I'd guess that OS X file associations only work with apps and not standalone programs. If so, they you are out of luck.
And note that copying things out of the .app package will not work. You have to use the /usr/bin/ebook-viewer link created by the install command line tools button.
As for the app store, calibre is GPL, which means apple's store is a no-go land.
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