I suggest to move controller.xml and portlet.xml under portal/ directory.
idm, jcr and jgroups already have their directory, why not portal ?

this would imply making this change in configuration.properties:

# navigation controller file
gatein.portal.controller.config=${gatein.conf.dir}/portal/controller.xml

# global portlet.xml
gatein.portlet.config=${gatein.conf.dir}/portal/portlet.xml