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It will create the CMakeLists.txt file (actually it just create a symbolic link in the src folder of your workspace pointing to CMakeLists.txt -> /opt/ros/groovy/share/catkin/cmake/toplevel.cmake in the case you're using groovy).

You don't need that command now. When you create the the package, you can just run catkin_make and it do also the job of catkin_init_workspace, and that's why sometimes it's not mentioned as you said.

Check out catkin tutorial