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This is sometimes caused by repository corruption - or at least, something in the history that the libraries we use don't like. I'd suggest making a fresh clone of the repository, and then trying linking again.
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So it would seem that linking the database using the Custom option, and selecting GIT resolved.
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"remote:internal server error Exception of type 'Sharpen.EOFException' was thrown."
I've upgraded to the latest version of sql source control and the problem persists. Any ideas?