so easy as 5 simple steps :

• Download and unzip new sonarqube-4.0.zip : > unzip sonarqube-4.0.zip -d $NEW_SONAR_HOME
• Manually edit sonarqube-4.0/conf/sonar.properties and sonarqube-4.0/conf/wrapper.conf and copy old properties values from old sonar conf
• Copy extensions from old sonar to the new one (only extensions not having correspondent in the new sonar)
• stop old sonar and start the new one :

  $OLD_SONAR_HOME/bin/yourOS/sonar.sh stop
  $NEW_SONAR_HOME/bin/yourOS/sonar.sh start

• Go to http://localhost:9000/setup (assuming sonar listen in localhost) and finally click under upgrade button