All of these structural aspects of an organisation can, like the organisation itself, be addressed and involved in workflow in the same way as a trust group, or member of a trust group. In fact every concept (node) in the Ontology is a trust group that has members and a direction it's evolving towards.
This structure can change according to the needs of specific groups, for example, an individual member or project will most likely not require separate departments. And in some cases there can be more appropriate words for the structural categories, for example, in the context of Self organisation, the category that's normally called a "department" is called "area of focus". Groups can use splitting & merging processes to change the granularity or diversity of an operating system "in the field".