Not sure if this is JGit's issue but it looks as though Bamboo's git plugin uses of version of JGit internal to Atlassian, so I'm opening it here.

When static initializer (lines 105-117) of org.shaded.eclipse.jgit.transport.Transport:

static {
	// Registration goes backwards in order of priority.
	register(TransportLocal.PROTO_LOCAL);
	register(TransportBundleFile.PROTO_BUNDLE);
	register(TransportAmazonS3.PROTO_S3);
	register(TransportGitAnon.PROTO_GIT);
	register(TransportSftp.PROTO_SFTP);
	register(TransportHttp.PROTO_FTP);
	register(TransportHttp.PROTO_HTTP);
	register(TransportGitSsh.PROTO_SSH);

	registerByService();
}

is called, TransportHttp.PROTO_FTP and TransportHttp.PROTO_HTTP aren't initialized yet and are added to the protocol list as null references.

We depend on using the HTTP protocol for performing different operations on GitHub via HTTP and since the constant is package protected, we can't register it ourselves without resorting to less desired methods.