Add remote via JGit
There are classes to add new ones:
RemoteAddCommand remoteAddCommand = git.remoteAdd();
remoteAddCommand.setName("origin");
remoteAddCommand.setUri(new URIish("http://github.com/user/repo"));
remoteAddCommand.call();
There is a RemoteSetUrlCommand
too.
Managed it to work that way:
Git git = new Git(localRepository);
StoredConfig config = git.getRepository().getConfig();
config.setString("remote", "origin", "url", "http://github.com/user/repo");
config.save();
And aparently it works like a boss.