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I suspect there is something in the plugin which is attempting to rewrite the URL and is adding the extra slash.
I think the syntax ssh://user@hostname:relative_path/repo.git is ambiguous, though it seems to be understood by git.
I use ssh://user@hostname:port_number/absolute_path/repo.git to allow my Jenkins job ssh access through port_number to a git repository on hostname at /absolute_path/repo.git. On my computer named "wheezy64b", I specify the URL as ssh://mwaite@wheezy64b:45022/var/lib/git/mwaite/jenkins/git-client-plugin.git
I can use ssh://user@hostname:ssh/absolute_path/repo.git to allow my Jenkins job ssh access through the ssh port to a git repository on hostnanme at /absolute_path/repo.git. On my computer named "mark-pc1", I specify the URL as ssh://mwaite@mark-pc1:ssh/var/lib/git/mwaite/jenkins/git-client-plugin.git
I'm impressed that the git command recognizes the relative path, since it seems like my second syntax (using the word "ssh" for the ssh port number) creates a conflicting case with your relative path case.
I agree that this is a bug in the git plugin or the git client plugin, though considering the ambiguity in the ssh URL syntax, I don't think I will ever work on fixing that bug. The fix would need to identify those cases where the plugin rewrites the URL and intentionally decide not to rewrite the URL, at least for this case.