Jenkins is installed using distribution (apt-get install jenkins) but is configured to run inside tomcat6.

In order to preserve default package location I added a symlink from /usr/share/tomcat6/.jenkins to /var/lib/jenkins

After this I change the default ownership for the /var/lib/jenkins from jenkins:adm to tomcat6:tomcat6

The problem is that after each Jenkins upgrade the server will refuse to restart because the permissions on the /var/lib/jenkins are reset and as a direct result it will fail to start because it cannot write to the /var/lib/jenkinks directory.