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You are correct that the git plugin and the git clone command have different results. The git clone command has more ways in which it can hang due to authentication issues, so the git client plugin has been implemented to use a combination of "git init" and "git fetch". That has fewer ways of hanging due to authentication issues and can be better managed.
Can you describe the use case which you're using that requires use of the "git clone" command rather than "git init" and "git fetch"?