/usr/include contains data about your packages, which means that a fresh install wouldn't write anything to it. I'm afraid your system has suffered a great loss.

Maybe you could try an update for your packages, but from experience, I know this doesn't usually work with Ubuntu.

sudo apt-get update

sudo apt-get upgrade

If your lucky, the apt cache will still have information about packages that used /usr/include. You can find a list using dpkg -S /usr/include/*, and use sudo apt-get reinstall [package] to fix things.

Edit : Best solution found in the comments :

sudo apt-get install --reinstall $(dpkg -S /usr/include/*|cut -d':' -f1|tr -d ','|tr '

' ' ')

In order to reinstall all packages that where corrupted.