/opt/ros/groovy/stacks/geometry_experimental/tf2/include/tf2/LinearMath/btQuaternion.h

Your eclipse-property setting only goes up to: .../geometry_experimental/tf2/include, but I think it should also include an additional tf2 directory.
You could also try to compile the package directly from the command line with rosbuild to see if that works. If so, then maybe you just need to re-run make eclipse-project and see if that fixes things.