Customizing your own FreeDOS cdrom is a two step process.
First, see the following page for how to first create a FreeDOS bootable cdrom:
Installation.BootDiskCreateCDROM
Second, before running mkisof from the first step, you'll need to edit the FreeDOS configuration files to your liking. Or, just create a subfolder containing the added files. Personally, once the cdrom drivers are loaded, I prefer just switching cdroms with the cdrom containing my own files.
(*See note below)
(*Edit Me! I've only created by own bootable FreeDOS cdrom. Adding files to the FreeDOS cdrom may require further uncompressing filesystem image files depending on if you want your files loaded into and made readable from memory as many of the other FreeDOS system files are. There are a couple of websites containing info on editing the configuration files already -- such as FreeDOS self-updating BIOS cdroms.)
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