Use SuperBuild/ directory as root directory

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We have a fairly common SuperBuild setup where the SuperBuild/ subdirectory contains ExternalProjects to compile dependencies and the main project (code is here https://github.com/SuperElastix/SuperElastix). Usually the build is started with "cmake src/SuperBuild" where "src" is the root directory of the project. How do we achieve this with CLion? We would like to have src/ as the root directory, otherwise CLion only shows the files in the SuperBuild/ directory.

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Essentially what I would like to make CLion do this (when pressing the CMake reload button)

 
/Applications/CLion.app/Contents/bin/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Debug -G "CodeBlocks - Unix Makefiles" /Users/kasper/Development/SuperElastix/SuperBuild
 
(notice the SuperBuild directory at the end) instead of this
 
/Applications/CLion.app/Contents/bin/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Debug -G "CodeBlocks - Unix Makefiles" /Users/kasper/Development/SuperElastix
 
(current behaviour). 
 
I have used the "Change CMake root" option, and set the root to the SuperBuild/ folder in the source directory, but this does not change anything.
 
The desired behaviour is achieved if the SuperBuild/ directory is selected when opening the project, but then all the files in the parent directory (which is the root of source tree) is not shown, of course.
 
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