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I sort my applications in separate folders within the Applications folder (e.g. One for my photo related apps, one for my guitar playing related apps, one for my video related apps, etc).

Since some of the system applications in OS X, namely Garage Band, iPhoto, Photo Booth and iMovie, fall under these categories, and I didn't want to clutter up my Applications folder I copied them to these subfolders and removed them from the Applications folder using Terminal.

However, whenever there is an update for them, I must first move them back to the Applications folder and then repeat the process.

Is it possible to "tell" the App Store where the Applications actually are?

Thanks in advance

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I could not reproduce this. Could you post the actual commands you use to move the apps? Also, did your Garage Band and other apps originally come from the App Store and have always gotten updates through the app store, or were they originally updated through Software Update? –  Alan Shutko Oct 12 '12 at 20:06
    
Originally they were updated through software update, and incidentally, my iPhoto (9.3.2) tells me there's a 9.4.1 available, but even when moving it back into the Applications folder the App Store doesn't show any available updates. Anyway, as for the commands, I simply drag-and-dropped the Applications to their new folders (thus creating copies) and then sudo rm -r'd them from the Applications folder. –  Francesco Zeno Oct 12 '12 at 20:14
    
I think there's a difference between App Store downloaded apps, and Software Update ones (which are shown in the app store list but still use the same technology). App store apps use spotlight to find the app wherever you've moved it, but I think the older apps are more tied to a location. Might be worth digging into how software update finds software. I'll try to check. –  Alan Shutko Oct 12 '12 at 20:27
    
From what I understand, as of Mountain Lion, software update no longer exists, in fact when iPhoto prompts me with "Open Software Update" due to the available update, I get sent to the updates section of the App Store. Also, iMovie, iPhoto and Garage Band all three appear as "Purchased". –  Francesco Zeno Oct 12 '12 at 20:34
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You're right, Software Update the application no longer exists. But as far as I can tell, for OS updates and older apps, the App Store app still uses the old Software Update servers, installer packages, and technology for finding updates. That's why I think that looking at how the old Software Update process worked might be helpful. (Here's one reason I think so.) –  Alan Shutko Oct 12 '12 at 20:38
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