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The MSVC tool collection does not work because windows paths are mangled. The paths are not truly converted into true cygwin paths, so there is no hope of them working. For example the include path Q:/CUDA_2_1/include is mangled into /Q/CUDA_2_1/include cygwin has a utility to convert between windows and cygwin paths. For the MSVC Tool collection, the paths should not be converted if they are in short (dos) form. The spaces, semi-colons and backslashes in long windows form are also tricky, and can often benefit from conversion into short form. This is related to another issue, where MSVC needs various values set in the environment, and needs them in windows or dos form.
Related to issue 158867