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I just upgraded from Snow Leopard to Mountain Lion. Now when I open my application folder via the Dock there are different programs present, e.g. Automator, which I moved to the "Utilities" sub-folder on Snow Leopard.

If I try to move them again to the sub-folder I get the message that the application cannot be moved to this sub-folder since the sub-folder cannot be changed.

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Moving system applications around is generally not a good idea. If you want to organize applications I suggest using Launchpad or a folder with aliases/shortcuts. – Gerry Aug 5 '12 at 19:01
But this shouldn't be a problem at all. I did this on SL in the same way and it never crashes. For me it's strange that just some of the system apps are directly in the program folder and most of them still in the utilities sub-folder (it is a system folder) as I ordered them on SL. I realy don't want to have programs like automator, app store or even the DVD player directly in the program folder but in the sub-folder – Daniel Aug 5 '12 at 19:09

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You can still do something like sudo mv /Applications/DVD\ Player.app /Applications/Utilities/.

I ran into several issues after moving applications on 10.6. For example Console crashed on launch, even though that stopped happening on 10.7. And OS upgrades will add duplicate applications at the original locations as in your case.

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I "solved" the problem by performing a clean installation of Snow Leopard and upgrade to Mountain Lion afterwards. Maybe this is not the most common way but now I don't have duplicated apps. Furthermore, I'll leave the apps where they are now and don't care that much about it anymore.

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