Back in the day there was ARP, the AmigaDOS Replacement Project (or AmigaDOS Resource Project). See
http://aminet.net/package/misc/antiq/ARP_13 and
http://aminet.net/package/dev/misc/ARP_13dev.
ARP was originally intended to replace the BCPL DOS commands of Workbench 1.x with equivalents written in C. So if you were just looking to replace the Commodore commands on boot disks you could look into using the ARP versions. Sadly ARP was never open source though. (Anyone know how to contact one of the former ARP developers? It would be interesting to get hold of the ARP source.)
At one point, some people believed that even distributing a bootable disk, made bootable with the C:Install command, was not allowed due to the tiny amount of code in the bootblock. So there were at least a couple of Install replacements which wrote slightly different code to the bootblock.
Anyway... today there are also the AROS commands which are open source. I haven't tried running any of the AROS M68K commands in AmigaDOS but they should probably work. (But only for Kickstart 2.0 or later.)