I haven’t had a great solution for a while, but I do use Eclipse w/ ‘eclipsify’ to help get a lot of the references working (still build with catkin tools though).
For anyone using Eclipse (who hasn’t already battled to set it up), I highly recommend ‘eclipsify’ from ethz-asl, to give you a jump-start in creating configured Eclipse projects for your catkin pkgs:
I just checkout eclipsify (and their other dependency catkin_simple) into my ws, build, and run the tool over a catkin list of the projects I have checked out, and it will generate eclipse projects for you to Import, which start with some good settings they have discovered. You probably want to make a separate ‘/projects/’ dir to output the projects into, rather than the default ‘/devel/’, so a clean doesn’t blow away your projects.
I still tweak it a bit, but it resolves a lot of the dependencies, which I find one of the most useful IDE features for me personally: I make sure to setup ‘Share settings/resources between projects’, make sure the C++11 flag is set, and include the /opt/ros/ include+lib dirs for my main projects, to help the resolution along.