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Although MS-DOS remains resident, my understanding at least is that Windows 9x is still an operating system and not just a shell because doesn't use the dos calls for what it does. For example, it implements 32-bit disc algorithms, unique video algorithms, it manages the keyboard on its own, it basically does everything and it just happens to do it on top of MS-DOS as a bootloader.

I believe there was an equivalent under linux called loadlin that would let you bootstrap Linux from dos, and it even let you use some ms-dos drivers to provide functions for unsupported devices like cd-roms, just as windows can gain functions from media device drivers despite ideally running pure windows drivers instead.
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Yes I am. I started the research for my next book a little while ago, and that's what I found. I was surprised that despite living on top of DOS 7, win 9x was a fully fledged OS and not just a shell on top of ms-dos.