Apps don't have access to their data anymore

Yesterday, to be able to follow evolution in the size of my Applications folder, I decided to add its actual size (4.5 GB) to the name "Applications".
It did not take very long before I realized I had made a big mistake. All my apps were behaving as if I were using them for the very first time. They were all empty of their data. I then renamed the folder to its original name "Applications". But that did not change anything.
What gives me hope that this problem can be solved is that I can see in different Libraries that the data is still there. For instance, the folder Home>Library>Caches>Metadata is filled with hundreds of icalevents. And if I click File>Get info, I can see the title of the event and its due date. But iCal remains empty as an application.
There must be a way to enable my applications to get back to their data, but I don't know how to do that.
Will someone please help me here? All my emails are gone from Mail, all my photos are not in iPhoto anymore etc...
Please, help me if you know how... I'm lost and frustrated.
Thank you!
biscotte
2.16 GHz Intel Core 2 Duo Mac OS X (10.4.7)
2.16 GHz Intel Core 2 Duo Mac OS X (10.4.7)

Do you have a recent backup copy of your boot drive? If so, your best bet is to recover the apps folder from your backup copy.

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