We have multiple projects setup in JIRA, however, we are using the WIKI on many projects, when a user who can only see the 2 projects they are assigned logs in, they can however click Wiki and view any of the other project spaces, any way to disable this or hide it to just users of that specific project?
You'll have to set up permissions in Confluence independently of the permissions in JIRA for this:
It's a good idea to setup groups per-project for this so you don't have to add/remove access on an individual basis.
You can also remove the wiki tab for specific users by removing their Confluence application access:
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