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The problem is that caktin_make calls cmake with -DCATKIN_DEVEL_PREFIX=/path/to/catkin_workspace/devel, but QtCreator is just calling cmake without any arguments. This causes catkin to place the develspace in the default location which is inside the build folder. You can probably add arguments to cmake in the QtCreator settings somewhere.

What I would do is build your workspace once with catkin_make, then open the CMakeLists.txt in the src folder with QtCreator and point QtCreator to the build folder created by catkin_make, then it should inherit all of the CMake settings catkin_make passed along.