You can't start Windows 9x directly from FreeDOS because Windows requires
the MS-DOS that it comes with.
What you can do instead is start GRUB4DOS from FreeDOS (directly from
FDCONFIG.SYS in place of a shell, without loading any drivers at all) and
use that to load IO.SYS, which will then load the rest of MS-DOS and
Windows as usual. Each OS will then have its own command interpreter and
configuration files: MSDOS.SYS/CONFIG.SYS/COMMAND.COM/AUTOEXEC.BAT for
Windows, FDCONFIG.SYS/FREECOM.COM/FDAUTO.BAT for FreeDOS.
I did that a few years ago and it did work.
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