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My coworker and I both recently updated to sourcetree 3.4.8.
Reproduction steps:
Create new tab
Click on "Remote"
Check "Show Organization Repos"
Click the pull down
Select the last project on the list (6th in our case)
Expected behavior: The one repository in the project should show up, allowing cloning.
Actual behavior: No repos are listed.
It doesn't seem to be a permissions issue, as we can clone the repo via the bitbucket server interface using the "Clone In Sourcetree" button and it opens in source tree fine. There doesn't seem to be any significant difference in the configurations for the project in question and the other 5 projects.