OS X :: CleanMyMac Deleted System Files

I wanted to delete from my desktop some useless for me files like some ipsw files downloaded earlier, pwnage tool, but when I wanted to trash those ones, CleanMyMac asked if I'd like to uninstall pwnagetool, I marked yes, because I thought that there may be some register files, than trashed the rest of files (cleared trash) and after rebooting my Mac seems to be formated, I mean whole settings, iLifes libraries disappeared, settings were zeroed but apps and data in Documents and Downloaded were the same. (I am almost sure that the problem was in deleting files with CleanMyMac), anyway at first I thought that was a glitch, recovered time machine backup and did the same, than restarted Mac - the same, now I am 100% sure about that, but I have to waiting another 6h with my very fast WD MyBook - because that time is required to wait with it if you want to recover 120GB, I wish I had TimeCapsule.