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When defining Extended Affiliations, the custom affiliations can be mapped to eduPersonAffiliations by selecting the appropriate value from the popup while adding or editing the custom affiliation. If a mapping is left blank, the eduPersonAffiliation will automatically map to an exact match (ie: student = student), otherwise a blank mapping is ignored.
Currently, this This mapping is only used by the LDAP Provisioning Plugin, which uses the mapping to populate the eduPersonAffiliation attribute, and the SQL Provisioning Plugin.