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I have Windows 7 64bit with 2 partitions:
C:, which is system partition (~100GB)
D: partition (~600GB) for programs

[I've changed in Windows Registry default directory for new installed software, which is: D:/Program Files for 64 bit software and respectively: D:/Program Files (x86) for 32 bit software.]

Unfortunately I needed to reinstall Windows 7 (only C: partition). After reinstalling it I figure out that I have nothing in Start Menu. Windows Registry was propably also cleared and I expect that I may have problems with programs installed on D: partition which may assume that they have already made changes in Registry (which is actually true, they did it, but I've formated C: and propably Windows Registry was simultaneously cleared).

I want my Start Menu content back. How can I deal with it?

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You have to reinstall all of your programs. Doesn't matter that they are on the D drive; your new Windows installation knows nothing about them. – Robert Harvey Aug 6 '12 at 17:21
    
So I am assuming the question you have is how can you restore those program shortcuts and settings? If so I believe it would be easier to just re-install the applications. Or, you could start using portable versions of those apps whenever possible so that you won't need to re-install most of them whenever you need to format. – Canha Aug 6 '12 at 17:21
    
When you get everything re-installed, make an image of your c: drive, using Norton Ghost or something similar. Restoring from the ghost image will retain all of your program settings. – Robert Harvey Aug 6 '12 at 17:24

You need to reinstall your programs I'm afraid.

You may have moved your programs to a different partition, but by reinstalling C: - you've blanked and rebuilt the OS. Your new OS doesn't know about your programs - to the new version of windows, they're just files on a drive.

The reason for this is that when you reinstalled your OS, you blanked your registry.. which sits on C: and is where your application list is hosted along with a lot of config info needed to launch various programs.

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