I've written a chroot wrapper for a Sauerbraten servers. Look for "sauer-server-jail" on my Sauerbraten page:
http://home.austin.rr.com/selliott4/sauerbraten/
which may be helpful for comparison.
Also, I used "strace" to determine which files were being read and written to. Something like
strace -f -o nexuiz.out -f -e'open,stat' ./nexuiz-linux.sh
might do it.