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This is an issue with CMake's install: when used to install a directory structure with files following a certain pattern (in this case headers, i.e., *.h, *.cuh, and *.hpp) it will duplicate the entire directory hierarchy, including creating empty sub-directories (if none of their files match the pattern).
If you have updated the Google benchmark and test submodules, when installing you will get their respective headers in the right sub-directories (but you also get several empty sub-directories).
If you did not update submodules, you will not have the Google benchmark and test code in your source tree to begin with (just two empty directories under src/chrono_thirdparty). You will be able to configure and build Chrono (albeit the unit tests and benchmark tests will be disabled), but on install CMake will generate those two empty directories.
I don't know of a workaround for this CMake issue without ugly hacks.
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