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Ammendment: running the downgraded config mentioned above loses all build history as exception being thron on all jobs when jenkins load builds build.xml with git entries causing the problem.
So now running Jenkins to 1.542 with git client plugin back to 1.6.0 and git plugin back to 2.0 and history back but git config file back to only being partially cloned.
As a workaround for now I have changed the part of the build that relies on these entries being in the git config file to reference the parts I need from the Git Environment variables.