The AAM deployment scripts replace /data/* with a new directory structure from a template after running ant on a clean deploy. Because of this, the deployment scripts need to be change to copy the init.xml file created by the ant build to /data/jirastudio/home/ after /data/* is replaced. This needs to happen on an upgrade deploy too.

Something like this:

# Copy init.xml if it doesn't already exist
if [ ! -e /data/jirastudio/home/init.xml ] ; then
    echo "Copying init.xml"
    cp /opt/jirastudio/build/current/init.xml /data/jirastudio/home/init.xml
fi

It's important that the file should not be replaced by the one from the ant build if it already exists, as the trusted apps key pair will have changed.