Well, I hit another milestone... the POKEY chip on the Atari XEGS can be setup to send an interrupt when a key is pressed. After spending some time this evening figuring out how to orchestrate that, and getting re-accustomed to NitrOS-9's IRQ polling system call, POKEY is doing its thing and the OS is handling it right along. I can now type commands at the shell prompt and have them execute. Also, notice the scrolling is working as well.
Also, the kernel is now scanning modules from $C000-$CFFF and $D800-$FFFF, skipping the $D000-$D7FF I/O range. It takes a few extra steps to build a ROM image to cope, but usable ROM space for NitrOS-9 is now up to 14K.