Instances are separate. Files stored in SharePoint are not in the version control library and vice versa. There is a web interface to the version control library that is available outside of SharePoint.
Each team project in TFS has an associated SharePoint portal. What we do is version control all of our software in TFS and save all our documentation on the SharePoint portal, which corresponds to the team project. We have definitely enabled version control in SharePoint so that we can get previous versions.
In the odd case, we need version control documentation along with the source code (for audit reasons), we will save this in the documentation folder in TFS.
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