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This is happening to quite a few people on our team. While on Sourcetree 3.1.3, users can see repositories that they have permissions to in the remote tab. When they update to the latest version of Sourcetree (3.3.6), all repositories stop showing up in the remote tab.
We were able to get the user's remote repositories (on 3.3.6) to show up by giving them read permissions to a different project. Both the repos from project A and B now showed up. This seems like a bug with Sourcetree. Has anyone found a solution to this?