Ahhhh..... handy. Thanks. I finally figured out what happened. Somehow someone changed their password to something stupid and we were hacked. Whilst being hacked a linux virus was installed. Then when our virus scanner ran, it detected and oh so helpfully removed all the infected files. Of course, all the files that I use regularly were infected, like chmod, ls, bash, cp.

In light of this it was far easier to reinstall from scratch to make sure that everything is gone.

Thanks guys.