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I think you're on the right track. I would create a new catkin package and add the executable and all its source files to the CMakeLists.txt file. You can also add any non standard library dependencies and compiler flags if you need to. You should be able to compile the same project without any code changes, so within catkin but with no ROS calls to test everything is working.

Then you can start adding the ROS functionality you mentioned.

You can edit the new source directory in eclipse by adding an 'existing source repository'. Personally I build my packages on the command line but you can setup build and run commands within eclipse if you want.