I also use Eclipse in combination with catkin tools (
http://catkin-tools.readthedocs.io/en/latest/installing.html), the config is set to create eclipse projects:
catkin config --cmake-args -G"Eclipse CDT4 - Unix Makefiles" -D_ECLIPSE_VERSION=4.6 -DCMAKE_BUILD_TYPE=Debug
This then creates a single project from each ROS package in the build folder of the workspace. In Eclipse you just need to import those you want to have in your workspace.
For me this is the best and easiest way to use Eclipse with ROS I discovered so far.
Using the normal catkin_make with the arguments above, you will always import all the packages in the workspace as one huge Eclipse project, which is not so nice in my opinion.
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