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The problem is upon configuring a job using an HTTP-based URL with Git credentials, the plug-in attempts to do form validation and verify whether the HTTP authentication succeeded. Because of the recent updates to store this info as a temporary store so that subsequent Git commands will succeed with these credentials, the validation can fail in the absence of a workspace directory.
In other words, the warning message "Failed to connect to repository : Command "git config --local credential.helper store" appears and can be ignored, but it's a false alarm. The job will fetch correctly if ran.
For instance, if Jenkins was started from the / dir, then git will attempt to access .git/config from the root directory, resulting in permissions denied.
Should the creation of the local credential simply just not be done in the absence of a workspace directory? See:
https://github.com/jenkinsci/git-client-plugin/pull/97