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To enforce the create-drop hibernate option I need to shutdown tomcat(?), however if I were to do that my jenkins server is also shut down. At the moment the jenins job simply builds the war and then copies it to webapps directory.
I want to enforce the create drop hibernate option on my web app without restarting tomcat/jenkins, is their a way to do this ?
As other users already stated you do not have to restart tomcat in order the restart a web application inside it. There is a deploy plugin available in Jenkins which is perfect for your scenario: https://wiki.jenkins-ci.org/display/JENKINS/Deploy+Plugin .
By the way, Jenkins comes with an embedded Jetty server so it is very straightforward to run this outside tomcat:
https://wiki.jenkins-ci.org/display/JENKINS/Starting+and+Accessing+Jenkins
In case you are just starting with this application then consider using Liquibase to manage your DB creation, upgrades, …: http://www.liquibase.org/ . It can be integrated with hibernate if desired and you could then easily create a Jenkins jobs that does a liquibase drop_all/update to recreate your database (schema) without touching your running application.