Well, I would scrap the groups_units HABTM association, as it isn't
really a direct association. You can't add/remove those associations
directly, so it's really just a symptom of the main Group ->
Department -> Units association.
Now, to get the associated group ids from a unit, have something like:
$this->Unit->recursive = 2; // get the Departments, and the
Departments' Groups
$unit = $this->Unit->read(null, $unit_id);
$group_ids = Set::extract($unit, 'Department.{n}.Group.{n}.id';
$unique_group_ids = array_keys(array_flip($group_ids));
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