So I wanted to try the new Android Studio and imported my eclipse projects (I generated a gradle build file). Worked pretty good.
The only library which does not see
If you don't have problems compiling and just after seeing the generated classes in the IDE, then you need to check if target/generated-sources/annotations is checked as Source Folder.
That would be File > Project Structure > Modules > Sources Tab, then look for the folder and tag it as Sources. The folder will turn blue and will be listed on the Source Folder list.