I thought I should post this so anyone who has this problem finds it.
I upgraded to phpstorm3 and when I opened my project, there were no directories. Alll the files in the rootdirectory were there though. It took me quite some time to find out that my older version of PHPStorm didn't properly index all the directories when I had it running the last time....
Si the fix is: open the older version, let it index everything, close it and open phpstorm3.
Hope this spares someone some time ;)