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I don't quite understand. Why use a janky, lossy Linux emulation layer when you can just target Windows natively?

For some reason git for windows is a cygwin build.

Because git expects a POSIX API and POSIX tools and also POSIX behaviour like symlinks and line-endings to do its job.

It's a native build. Only various tools it is shipped with are cygwin builds, like bash etc.

Oh, indeed, but git often calls them.

Git for Windows uses MSYS2, which is a mix of a Cygwin fork and MinGW, the implementation of the Win32 APIs for Linux.

Cygwin is an ugly hack anyway.