I was just organising my music in iTunes and suddenly it said it couldn't find the file of a song (that I just played a minute before). Next an settings message came up that I had to sign in to iCloud again, and then a message came up asking me if I wanted to also remove all user data of Steam. All my alarm bells went of, something is seriously messed up here. I immediately turned off TimeMachine and WiFi as not to spread whatever is going on to the rest of the devices in my house. I went in to Console to see if it would give me any lead on what was going on, but the only odd thing I saw was all sorts of messages about files that couldn't be found (which is to be expected if everything suddenly disappears). I went to Finder and saw that all my user folders are empty except for Pictures. I thought maybe my Mac is having an off day so as a good computer user I tried turning it off and on again. When it booted I was presented the "Welcome to your Mac" setup process! I only had to do like two steps (sign in to iCloud and accept analytics stuff). Then I got back to my desktop and everything was as if I had just taken a new Mac out of the box. First thing I did now was changing my Apple ID using my iPhone (maybe someone remote wiped my mac using iCloud or something. Although I didn't find anything suspicious there.) I did some more looking around and found that most Apps where also removed, but not all (for example Microsoft Office is still there but MS Remote Desktop is gone. Dropbox is gone but GoPro studio is still here). All files from my mac are gone except for the contents of the Pictures folder and another folder I made myself in my user home folder (containing some software installers). I did some searching on the web but didn't find anything similar to my case. I would really like to know what caused this, I do have some backups but if I don't know what caused this then I can't be sure it won't happen again... I'm using a Retina Macbook Pro mid 2012 with the latest version of El Capitan. Any help would be greatly appreciated.