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The git-client-plugin 1.6.2 release again adds a remote section into the .git/config file. Could you check that this is resolved with git-client-plugin 1.6.2?
The repository is definitely not checked out as a bare repository. You can test that by creating a job which clones from your favorite location and then runs the command:
That will always report "false" for git repositories cloned by Jenkins since Jenkins needs a working copy of the repository and bare repositories do not have a working copy.