My GitHub account has both public and private repos, but only the public ones are listed in the New Tab -> Remote view. I can search and find my own private repos, but I can't list any repos (public or private) that I have access to, i.e. listed in the API call to https://api.github.com/user/repos. This also affects private repos in organizations I'm in, despite the "Show Organization Repos" checkbox. I am not a member of any organizations that have public repos, so I can't check that.
This isn't a deal breaker, because I can still use the Clone button, but the "Cloning is even easier if you set up a remote account" text is taunting me.
I had a similar problem; after adding my GitHub account to SourceTree, repos belonging to my organization weren't appearing in the 'Remote repositories' list. I tried starring the relevant one, but that didn't make a difference.
I discovered it was an issue with the default permissions in the OAuth settings; by default, it doesn't give organization access.
To fix, go to your GitHub settings -> Applications -> Authorized OAuth Apps -> Sourcetree ('SourcetreeForWindows' in my case): you can see the list of permissions granted, and underneath that Organization access, and the option to turn it on.
[This Medium article described the same problem and solution, except that they suggest deleting and re-creating the OAuth token, whereas I was able to just edit the settings on mine: https://medium.com/@johnnyfekete/accessing-a-git-repo-after-transferring-it-to-an-organization-99b1c78f5286 ]
(I'm not sure if is the same/similar problem to above, but I came across this question when searching for a solution, so thought it good to add my solution here after I worked out what my issue was.)
I'm afraid it's a while since I did this, so I forget the details. But certainly the repos I was concerned with were public ones, just that they belonged to an organization. So the commonality of my problem with the original question here was "organization repos not appearing" rather than the private/public dimension of the question. So it could well be that the solution for that is different.
However, I'd be surprised if it's not possible to access private repos at all this way. You may well have already looked here, but I found this on an initial google:
Is it just a private repo you're wanting to access, or a private organization repo? If the latter, from that first link I think an organization owner has to grant access for the app (so I guess even if you have access as a GitHub user, you don't automatically get access when using the app).
That may or may not be helpful, but I hope you can find a solution. And do post back here when you do!
The problem you are encountering sounds similar to the one I had. Take a look here for a workaround: https://community.atlassian.com/t5/Sourcetree-questions/Re-Sourcetree-for-Mac-GitHub-account-permissions/qaq-p/970146/comment-id/26875#M26875
Additionally, it might be helpful to upvote the issue here: https://jira.atlassian.com/browse/SRCTREE-6322
Thanks Boris, that helped a bit, but the workaround only gave me access to public repos of organizations I'm in, and didn't help with private repos of said organizations, nor my own private repos. I've upvoted the Mac issue, but I'll add an additional issue for Windows, since it seems that the functionality might be different, e.g. the initial OAuth request on Windows does request quite a lot of permissions.
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