Hi, We are having a problem with the Sync in Source Tree with the Unity Project, we are thinking are the meta datas, because every change one developer do, in some way is not update in other dveloper, always is missing a link connection, a folder, or maybe a folder of one developer still appearing when someone already delete it in few days. Do you know why is happening?, we are having delays cleaning and cleaning the Project.
I can almost 100% safely guess this has nothing to do with Source Tree.
I use git, source tree in mac and pc (among many other guis), and unity3d. I never had any such issue and can't think of how a GUI would make that happen. SourceTree is just a git wraper.
So, I suggest you begin with this checklist: http://docs.unity3d.com/Documentation/Manual/ExternalVersionControlSystemSupport.html and then review your git workflow. Cherry picking and merging can make unexpected merging behaviour, for instance, and it could cause things to "reappear".
If it's all checked right, I suggest posting a (then) more informed question on unity answers - as it's most likely the only thing that might be breaking stuff there. Git isn't the best versioning tool to integrate with Unity but I couldn't find a better one yet.
It is possible that some of your developers are deleting *.meta files. Check the logs.
You should set on all your Unity3D developer machines Version Control - Visible Meta Files mode and Asset Serialization - Force Text.
Also put under source control and share ProjectSettings\* across all the developers.
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