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The problem is that based on the first invocation of CMake the value of the SETUPTOOLS_DEB_LAYOUT determines SETUPTOOLS_ARG_EXTRA. These values are than cached and not changed anymore (until explicitly set by the user). This is even the case when you set -DSETUPTOOLS_DEB_LAYOUT=OFF which will not change the value of SETUPTOOLS_ARG_EXTRA.
As a workaround for now you can remove the CMakeCache.txt and run CMake again with the desired SETUPTOOLS_DEB_LAYOUT.
In the meantime catkin has been modified as stated in https://github.com/ros/catkin/issues/314 to always correctly update SETUPTOOLS_ARG_EXTRA when SETUPTOOLS_DEB_LAYOUT are changed.
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