Found it. You can supply custom configuration through the following xml (link to cargo docs in the above comments)
<files>
<copy>
<file>tomcat-users.xml</file>
<tofile>conf/tomcat-users.xml</tofile>
<configfile>true</configfile>
<overwrite>true</overwrite>
</copy>
</files>
So you can specify your own conf/*.xml or anything else and it will be copied before the container starts. I can login to the manager now :)
Cheers