CMake insists on creating the build directory, and it is annoying that you have to delete build directories all over the place when all you want to do is take a quick look at some sources. So creator "builds" in a temporary directory to extract information from CMake -- till you actually trigger an explicit build from creator. At that point the actual build directory is created and all the files go there.
You need to tell cmake to run your command in the source directory if those commands depend on being run from there: CMake usually does not build in the directory your sources are and will default to running stuff in the build directory.