You can configure a GitHub Enterprise Server for the GitHub Branch Source Plugin.

We'd like to configure a proxy for api.github.com/github.com that looks like my-github-proxy.com.

This URL is normalized as a GitHub Enterpise Server, with any trailing slashes removed:

GitHubConfiguration.java

 
And this causes `getRepositoryUrl` to create a URL like `my-github-proxy.comOrganization/Repo` instead of `my-github-proxy.com/Organization/Repo`:

GitHubSCMSource 

It would be great if we could either not normalize URLs like this, or allow for specifying both a checkout url and an api url.