How to configure the jira so the users on see only activity in the activity stream for projects they have access?
With access you mean 'Browse Project' permission. A User can only see activities of projects where he has that permission. So there is nothing you need to do.
It appears that the default permission scheme provides new users with access or permissions to all projects. As such I assume I will need to set-up a specific group and associated permission scheme with access to only those projects where the user has a role.
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