For those who were wondering...
What used to be in ~/.IntelliJIdea/config is now in ~/Library/Preferences/IntelliJ IDEA (thanks to Hani for pointing this out).
What used to be in ~/.IntelliJIdea/system is now in ~/Library/Caches/IntelliJ IDEA and yes, this includes idea.license which is a really bad idea if you ask me since Caches are susceptible to be removed at any time...
I filed a bug on that last point, see:
Hope this helps.