I've got one instance of Jackrabbit 2.6.5 running under Tomcat 7.0.42 on Ubuntu 13.10 by dropping the WAR into Tomcat's webbapps folder as jackrabbit.war.
If I copy the war file to jackrabbit2.war, it starts up a second instance at host:8080/jackrabbit2, but it seems to share the same configuration (and hence repo storage) as, if I create a workspace in one instance, my repo browser shows it as present in both.
Note that I've revised WEB-INF/web.XML to point bootstrap-config to /opt/jackrabbit/bootstrap.properties (for both Repository and RepositoryStartup), and bootstrap.properties to with repository.home=/opt/jackrabbit and repository.config=/opt/jackrabbit/repository.xml for the first instance and made the same changes (but to /opt/jackrabbit2) for the second instance - so both repos should be using their own config and locations?
The reason for running multiple repos (whether under one or many Jackrabbit instances) is so that I can configure them with different backends for testing.
Is there any way of doing this? Do I need to tell Tomcat these are not the same app, or something? Or have I missed something in my configuration?