To expand on why CHKDSK itself can't deal with FAT32, Freedos tries to retain
compatibility with quite a broad range of hardware, including both any 8086
machines that anybody still has lying around, and modern hardware. So CHKDSK
has to be able to be able to work on 8086s. This means that it can't depend on
the availability of anything more than 640k of conventional RAM, which makes it
difficult to deal with FAT32, and such machines are unlikely to have disks big
enough to need FAT32 anyway. Thus there is a separate tool, ported from Linux,
to deal with FAT32 on beefier machines (i.e, most hardware released since 1990
or so).
Microsoft didn't have this constraint when they released FAT32 with Win95, as
they'd already determined that Win95 would not run on machines that old, so MS
CHKDSK has been able to deal with FAT32 since it was released.
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