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I was running the Tweetbot for Mac Beta, and still had it installed when I installed the full release from the Mac App Store.

Now I have 2 entries in my preferences for Notification Center, and I don't know which is which. I have removed the Beta application, and only have the real thing installed, but oddly whereas the Beta had the 'Egg" icon rather than the bird, both set of preferences use the bird icon.

Where does this preference pane get it's information about installed applications? How can I remove an app from the list?

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I too have this issue. I've even tried deleting Tweetbot, but one of the icons still remains. Most likely the beta one. I don't know how to get rid of it. –  Jako Nov 8 '12 at 16:11
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Open terminal and run this command:

/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -kill -r -domain local -domain system -domain user && pkill Finder

Or, if you have OnyX utility app, go to "Maintenance" > "Rebuild" > check on "LaunchServices" (leave the other options unchecked) > execute

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