I have modified Atlassian script to support following features:

• Cleanup for leftover files – .jira-home.lock, catalina.pid
• catalina.out log backup
• Check for running process and force kill JIRA if it won’t stop on time

#!/bin/sh -e
# JIRA startup script
# Description: For JIRA 7.2.7

# Define some variables
# Name of app ( JIRA, Confluence, etc )
APP=jira
# Name of the user to run as
USER=root
# Location of application's bin directory
BASE=/u01/jira/Prod_7.2.7
export JIRAHOME=$BASE
# Location of application's home directory
JHOME=/u01/jira/Prod_7.2.7_home
export JIRA_HOME=$JHOME
# Location of Java JDK
export JAVA_HOME=/usr/java/default

case "$1" in
  # Start command
  start)
    echo "Starting $APP"
    lockfile="$JHOME/.jira-home.lock"
    [ -e $lockfile ] && rm $lockfile

    pidfile="$BASE/work/catalina.pid"
    [ -e $pidfile ] && rm $pidfile

    logfile="$BASE/logs/catalina.out"
    [ -e $logfile ] && mv $BASE/logs/catalina.out "$BASE/logs/catalina-`date +%F`.out"

    /bin/su -m $USER -c "cd $BASE/bin && $BASE/bin/start-jira.sh &> /dev/null"
    ;;
  # Stop command
  stop)

    blah=""
    temp=`ps aux|grep java|grep jira|grep -v grep|awk '{print $2}'`
    pidfile="$BASE/work/catalina.pid"

    if [ "$temp" == "$blah" ]
    then
       echo 'JIRA is not running'
       exit 0
    fi

    echo 'Shutting down JIRA'
    /bin/su -m $USER -c "$BASE/bin/stop-jira.sh &> /dev/null"

    echo 'Sleeping 30 seconds, because sleeping is good...'
    sleep 30 

    temp=`ps aux|grep java|grep jira|grep -v grep|awk '{print $2}'`

    echo 'Now checking if JIRA is still running...'

    if [ "$temp" != "$blah" ]
    then
       echo 'Force killing JIRA now...'
       /bin/su -m $USER -c "$BASE/bin/catalina.sh stop -force $num >/dev/null 2>&1"
       echo 'Killed'
       exit 0
    else
       echo 'JIRA is already down'
       exit 0
    fi

    echo "...done"
    exit 0
    ;;
   # Restart command
   restart)
        $0 stop
        sleep 60
        $0 start
        ;;
  *)
    echo "Usage: jira {start|restart|stop}"
    exit 1
    ;;
esac

exit 0