Hi Samy,
They moved it to the .eaglerc is now version specific and located in ~/Library/Application\ Support/Eagle/settings/x.y.z/
I found the loss of the directory setup when I installed it too. Fortunately you can open up 9.0.1 and copy/paste between the two and get everything back. They have changed the directory setup stuff slightly. All the EAGLE system specific ulp/scr/etc have all been classified as "examples" and all moved into examples folders and there is a new checkbox to enable/disable examples. Then by default these are read only and there is new user space equivalent locations for people to put their own ulp/scr/etc. I think this latter change to by default provide a distinct separation between core system files and user space files for these is long over due, the other stuff with everything being moved around and classified as examples isn't right and I am seriously not convinced about separating the .eaglerc into per version settings. It makes switching between versions if anything has changed in terms of project folder structures etc, very painful and defeats the original point of having this file, so settings persist between versions.
Best Regards,
Rachael