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Looks like Git plugin based on JGit is not observing environment variables like 'HOME' and not defaulting HOME to HOMEDRIVE\HOMEPATH in Windows.
Note that Node and/or Job configurations can modify these environment variables - this case needs to be handled too
In particular: SSH config location needs to be based on 'HOME' at the level of the job (defaulting to HOMEDRIVE\HOMEPATH in Windows if not set), same with Git configuration