If the renaming does not work, this may be due to the fact that your project will not be successfully created. Try this with a simple project, for example. create a brand new Hello World program. I am sure that if it works successfully, refactoring will work. Worked for me in CLion 1.2.4 on OS X 10.9.4.
As for CMakeLists.txt , this is a standard file that CLion automatically creates if you create a new project. If you have an existing project, you will find CMakeLists.txt if you open the menu View->Tool Windows->Project .
My advice is to experiment by closing an existing project ( File->Close Project ), creating a new project and playing with CLion functions. Here is a nice Quick Start Guide for CLion
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