Better late than never, I just put this together for the 990 update. You put the script in the directory that your executables live, but you run it from the top level of your source directory (e.g. "EQEmu-0.7.0-990"). I call this "update-server", I also have a "restart-server" script which is the same with the three "cp" commands cut out.
Code:
#!/bin/sh
SERVER=/your/server/binaries
killall eqlaunch
sleep 6
killall -9 zone
sleep 1
killall world
sleep 6
cp zone/zone world/world eqlaunch/eqlaunch $SERVER
cp EMuShareMem/libEMuShareMem.so $SERVER
cp utils/*.conf utils/cleanipc $SERVER
cd $SERVER
./cleanipc
sleep 2
nohup ./world &
sleep 10
nohup ./eqlaunch zones &