We've recently imaged 5 identical OSX Yasomite macbooks with sourcetree on them.
They're all showing identical symptoms that it seems randomly after a period of time or restarting, the bookmark manager displays every repo as missing and you need to relink it.
The folders are not moving and nothings changing, and once you relink it, it works again for a period of time.
Might be worth noting that the users are not admins or in the sudoers file.
Well, that sounds like a good place for them to be. Are these macbooks each being used by multiple users? If so, maybe SourceTree isn't storing bookmarks in a user-specific way (and has problems when trying to load repos from another user's Sites/ directory). If these are single user machines, you may need to submit a bug report to jira.atlassian.com, because that doesn't sound like any sort of user or configuration error.
Supported Platforms macOS Sourcetree has a lot to offer and, like many developer tools, finding and using it all can be a challenge, especially for a new user. Everyone might not love ...
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