But again, I think we can avoid this tortuous path and fix the CMake or
Makefile to build on Windows.
Fully understand.

It is likely that you could create a pure Windows native build (using a Windows native toolchain) or a pure Cygwin build (using a tool chain built under Cygwin) with CMake.  But I suspect that CMake would have difficulties with a mixed environment:  A Cygwin POSIX environment with a Windows native tool chain.  I could be wrong, but that is a perverse environment so I wouldn't have high expectations.

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