Hi, to create a very simple FreeDOS bootable system,
get the kernel from http://freedos.sourceforge.net/
(-32 version supports FAT32 as well, -16 version does not).
The download will contain a version of FreeCOM command.com,
too, and some simple examples for autoexec / config. It also
has the SYS tool which you need to make a disk bootable.

Use those tools to create a bootable FreeDOS floppy. Your
CD-writings software should be able to use an image of that
floppy to create a simple bootable CD-ROM. After booting from
that CD-ROM, the image will look like a normal floppy drive
for DOS, but the rest of the CD-ROM will not be accessible
unless you load CD-ROM drivers. No real problem - FreeDOS,
FreeCOM and your BIOS images and flash tools should easily
fit on the floppy, so access to the rest of the CD-ROM is not
needed in that case.

I think loading HIMEM and using DOS=HIGH would be useful.
Loading EMM386 could cause problems with BIOS access, but
the documentation of the flash tools should tell you about
that.

A small FreeDOS distro - one floppy - is FreeDOS ODIN. It
comes as a disk image along with the DISKCOPY tool to copy
the image to a disk (in DOS or Windows - as with SYS), but
you can also use dd / ... to create a bootable disk from
the image in Linux. In that point, ODIN is easier to use
compared to normal "use SYS to make it bootable" FreeDOS
installations. You can remove unneeded tools to get enough
free space for the BIOS images and flash tools.

Last but not least you can find some more complex sample
configurations for "bigger installs" in
http://www.coli.uni-sb.de/~eric/stuff/soft/specials/freedos-config.txt

Eric

PS: To automate the BIOS update process, you could write
some batch scripts. Depends on how much the computers differ
among each other. If you have to take custom decisions for
each computer, you better run the flash tool by hand after
booting that FreeDOS floppy / CD-ROM.


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