Do files need to be upgraded too?

I just upgraded to Lion.
I store my files on an external back up drive.
Because I just upgraded, should I re-copy those files to the external drive? Or are they the same? Do they become Lion files?
Lastly, what is the best way to repair permissions after an upgrade, from the recovery partition or just via disk utility?

Most files do not need to be "upgraded." However, if you created them on an older piece of software that may not be supported again, it may be a good idea to convert them to something that will be readable in the future, if they are not in a format that can be read by current programs. Old AppleWorks files fall into this category.
You only need to repair permissions when you actually have a file access problem, and when you do so, from the normal boot drive.

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