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Trouble locating files after upgrading to Mountain Lion

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Just upgraded from Leopard to Mountain Lion. I backed up everything from Leopard once, then backed it all up again once Mountain Lion was installed. Now, I'm having trouble locating all my file folders... everything seems to be lumped into "All My Fi

Just upgraded from Leopard to Mountain Lion. I backed up everything from Leopard once, then backed it all up again once Mountain Lion was installed. Now, I'm having trouble locating all my file folders... everything seems to be lumped into "All My Files". How do I restore everything to their normal spots... so I can see all the normal folders?

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When you say you backed up and then backed up again, what does that mean?
Hopefully you knew that Time Machine will make changes going from Snow Leopard to Lion and above and you would have two sets (keep the old)
Ideal is to do CLEAN install on a newly formatted drive and use Setup Assistant to import or migrate apps and documents.
Another, to do a clone (CCC is great as it will create a Lion/ML Recovery partition) and let you keep dual booting for a month or until eve rything is WORKING and updated.
Finally, most learn that with the Mac Pro, isolate all the data documents media and library follders to a non-system disk drive. Handy. Better performance. Leave your home library on the boot drive, which unfortunately Apple saw fit to make hidden by default. I like to dig in and delete caches so now I am more likely to use CCleaner which works fine on Mac as it did on Windows, safe and no issues.
Never update over your only backup set. Not at first, maybe not ever, and always have multiple redundant backup methods (like CCC and Time Machine at minimum).
The files should still be on your backup sets if you were CAREFUL and did it right. And planned ahead a bit.

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