I ran into a problem where the Mac App Store said that a particular app (Numbers in this case) was up to date, but whenever I launched it I would get an older version. I finally did a search across the entire computer and found Numbers.app in a folder on an external drive. I have no idea how or why it was installed there instead of on the local hard drive. So I moved it from there to the Applications folder on the main internal drive and re-created the dock shortcut and now the correct version launches.
The problem is, now when I go to the App Store it says there is a new update available. So it appears that the App Store wants to use the external drive location and now that I deleted it from there it wants to put it back. Obviously I don't want this to happen: first of all, if the external drive goes away I would lose the app, and second, every time there is an upgrade it is going to cause more problems.
So, how do I get the App Store to correctly recognize that Numbers is installed in
/Applications, not on the external drive?