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You should take a look at the following page for a detailed explanation: https://confluence.atlassian.com/display/CROWD/Effective+memberships+with+multiple+directories
Let's suppose you have an application called JIRA and that you linked this application to two directories in Crowd, for instance Directory A and Directory B (in this order). Now, let's also suppose that each of these directories has two groups called jira-users and jira-administrators.
Now, let's suppose that user john_doe belongs only to jira-users within Directory A and to both jira-users and jira-administrators within Directory B.
From JIRA's perspective, if you do not select aggregating membership, john_doe will only be a member of jira-users. However, if you do select aggregating membership, john_doe will be a member of both jira-users and jira-administrators.