We've recently moved to using Tomcat's standard configuration format as a large number of users indicated that they'd prefer the format to be one with which they're already familiar. This means that we now have tomcat-server.xml instead of the old servletContainer.config file.
The absence of the context.xml, tomcat-users.xml and web.xml files is a temporary (and accidental) change. I've opened DMS-994 to fix this. Thanks for spotting this and reporting it.
The changes to the other configuration files are due to the fact that we're moving towards using ConfigurationAdmin for the vast majority of dm Server's configuration (with Tomcat configuration being one of the exceptions to this).