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CUDA/Clang: Fix separable compilation in non-root directories with Makefile generators

Raul Tambre requested to merge tambre/cmake:cuda_separable_clang_make into master

Seems the relative paths were wrong basically all around such that only compiling files in the top-level directory would work. I've modified CudaOnly.SeparateCompilation to cover this.

Fixes: #22482 (closed)
Backport: release

Edited by Brad King

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