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I recently had my hard drive replaced. I made sure my Time Machine backup was up-to-date prior to the handing it over to the Apple Store so I could simply restore, but I made one mistake: /Applications was not being backed up with Time Machine.

I got my computer back today, and I now have a fully restored iMac less /Applications. This means the Dock is full of question marks... I have nothing. I'm typing this from the restore partition where I don't see any way to replace /Applications.

All I can think to do from here is start with a fresh install and work from there. Any ideas before I go down that route?

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Here’s what worked for me: I restored Mountain Lion (via the restore partition) and it did not affect my existing user accounts. I had to redownload a few third-party apps but did not lose any data or have to start from scratch. Thanks for the help! – DehydratedSnowman Oct 21 '12 at 15:33

If you hadn't backed up Applications, you're stuck there. But you should be able to just go and reinstall the applications. When you do, the dock will be normal again and you'll have the benefit of keeping your settings and everything else. No need to wipe the whole thing and restart.

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How would you reinstall the applications? – DehydratedSnowman Oct 21 '12 at 1:25
From the original install media. Most of my software these days comes digitally, so I store all the dmg files off to an external drive (automatically via a Hazel rule) so I'd go through there one by one and just run the installer or copy them over. – Alan Shutko Oct 21 '12 at 3:28

First thing is browse the backup using Finder or the Time Machine interface and see if spotlight can find a missing app at a different time interval than the one used for the restore.

Unless you went in and excluded that folder from backups, those files are normally included in all backups, but perhaps there was a glitch in the backup or the restore and you can avoid having to manually reinstall the third party apps piecemeal.

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