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Atlassian supports SCIM to provision to Atlassian Access (free for higher ed) per organization
If you want the same groups provisioned to multiple applications, have the applications in the same Atlassian organization. If you want distinct groups in different products in Atlassian, create an organization for each product.
External users can be provisioned to groups in Atlassian. If the domain of the user is claimed and configured for SSO then the user will use their SSO. If not, then they create an account in Atlassian
To allow external users to log in with their SSO, you can have a SAML proxy (e.g. satosa), and use email forwarding
Users in Atlassian cloud have an email address which is the same as their login id
Note that the SCIM integration with Atlassian does not manage all groups in the organization. If there are groups that were created manually, they will not be available to manage over SCIM. Only the groups created by SCIM can be managed by SCIM
It seems that users cannot be updated by SCIM especially if they were created outside of SCIM
External system
Create a SCIM security token in Atlassian admin
Handling external users
This example shows how to use Grouper local entities to model external entities in Atlassian cloud.
If there is a user in Atlassian cloud who is not in a subject source, you can add an external entity and set the display extension.