Okay, I royally screwed up.
I was trying to install a new app to plug iPad up to Linux, as I used apt-get install xxx it poped up it was going to delete all the apps from my PC.. I accidently hit y instead of n and it proceeded to delete everything.. While I was unable to stop it.
I'm using the Live version now and my actual files are safe, how do I go about using the USB drive to repair the partition, that is.. Install the OS back without deleting my root documents folder like Windows does?
Any help would be wonderful so I don't have to go buy a USB stick, back up and reinstall.