remove cmake and re-install it
I removed cmake before and just found it also removed something in ros folder. After I re-install cmake, I was not able to use catkin_make command. Then I just followed the installaton tutorial of indigo again and tried to fix the removed part of ROS folder. Now I can use catkin_make but I found that the already compiled code is not compilable now. I have no idea about this.
Try to clean the build and devel folders in order to run a clean catkin_make.