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To clarify for khambuch: I used the solution provided by dgossow and the problem still persisted. At that time when I opened eclipse I used ~/workspace as my workspace while the Ros Project was in the directory ~/ros_workspace. I imported the project into eclipse without copying the files.
When I closed eclipse and re-opened it selecting ~/ros-workspace as my workspace and then importing the project into eclipse everything worked.
Eclipse saves its configuration inside the directory you choose for a workspace. By switching workspaces, I forced eclipse to establish a new configuration and then it worked as expected.
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