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gazebo6 from the OSRF repository declared conflict with gazebo2, so updating your system from just gazebo2 to gazebo6 should work out-of-the-box.

This situation is not the same if you have installed packages that depends on gazebo2 like ros-indigo-gazebo-ros-pkgs. What I would recommend, two options:

  1. Use aptitude (package manager, it propose solutions to conflict situations)

    apt-get install aptitude
    aptitude install libgazebo6-dev
    
  2. Clean up sdformat first, install later

    apt-get remove '.*sdf.*'
    apt-get install libgazebo6-dev
    

Both should resolve the situation.