Cory,
All the services can be installed outside the container or inside. But, for Redhat, you should install them outside the container as the inside there's some weird licensing issue.
In that case, the replication directories would be outside the chroot like so:
```
/opt/gluu-server-3.1.2/opt/gluu/jetty/identity/conf/shibboleth3/idp/
/opt/gluu-server-3.1.2/opt/gluu/jetty/identity/conf/shibboleth3/sp/
/opt/gluu-server-3.1.2/opt/shibboleth-idp/conf
/opt/gluu-server-3.1.2/opt/shibboleth-idp/metadata/
/opt/gluu-server-3.1.2/opt/shibboleth-idp/sp/
/opt/gluu-server-3.1.2/opt/shibboleth-idp/temp_metadata/
/opt/gluu-server-3.1.2/etc/gluu/conf/
/opt/gluu-server-3.1.2/etc/certs/
/opt/gluu-server-3.1.2/opt/symas/etc/openldap/schema
```
You can ignore the shibboleth directories if you don't have it installed and ignore the symas directories as well, if you're using OpenDJ.