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Is it possible to create a group per Atlassian product but still maintain the integration? We have Jira, Confluence, Bitbucket and Hipchat. Not all four products are necessary for all users, how do I separate this effectively?
Your instincts are correct, create an access group per application and put different people in them. This won't affect your integrations directly, but you may find users who have different accesses may see quirks (e.g. if a user has Confluence and looks at a page that reports on Jira, but they have no Jira access, the reports may look empty)
Just to add to what Nic has already stated. I would suggest you to use "crowd" for managing all the groups and being the single source of truth for authentication/authorizations to all the different applications because scaling user management schemes isn't an easy task especially in last enterprise setup.