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It may be a not so usual case, but it's a valid one nonetheless. I think that the plugin doesn't have to be "hacked" it just can also check the "GitHub project" setting to match incoming github hooks with Jenkins jobs. Maybe that's a more sensible default too. After all, an HTTP URL to the repo may be totally different than it's git url.
What do you think? Ι think the relevant code is here: https://github.com/jenkinsci/github-plugin/blob/master/src/main/java/com/cloudbees/jenkins/GitHubRepositoryNameContributor.java#L60-L74
The .gitconfig is irrelevant to this issue.