Create a user named "minecraft" and check out repository in its home directory.
sudo useradd -d /home/minecraft -m minecraft
sudo su minecraft
cd ~
git init
git remote add origin https://github.com/cal/a-minecraft-server.git
git pull origin master
Build stuff
cd ~/build
./update.sh
Deploy stuff you built
cd ~
./update.sh
Copy init/minecraft.conf into /etc/init/
sudo cp /home/minecraft/init/minecraft.conf /etc/init/
Start minecraft
sudo start minecraft
Set up a cron job for the minecraft user
# m h dom mon dow command
* * * * * /home/minecraft/cron/cron.sh