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You should never edit the boilerplate toplevel.cmake file. This code should be removed:

project(YOURROBOT_gazebo_plugins)

find_package(catkin REQUIRED COMPONENTS
  gazebo_ros
)

# Depend on system install of Gazebo
find_package(gazebo REQUIRED)

include_directories(include ${catkin_INCLUDE_DIRS} ${GAZEBO_INCLUDE_DIRS} ${SDFormat_INCLUDE_DIRS})

# Build whatever you need here
#add_library(...) # TODO

catkin_package(
    DEPENDS
      gazebo_ros
    CATKIN_DEPENDS
    INCLUDE_DIRS
    LIBRARIES
)

If I am following your example correctly then that means you have actually edited the toplevel.cmake template file located at /opt/ros/indigo/share/catkin/cmake/toplevel.cmake and you should make sure you fix that one too.