Echo, Flow, and a few other extensions use core's includes/utils/AutoloadGenerator.php to generate an autoload.php file that appends to $wgAutoloadClasses. As we convert to extension registration, this should be adapted to, e.g. load extension.json file, add the class map to its "AutoloadClasses" key, and write out the new extension.json.
Hi! Sorry I missed you on IRC. So I was imagining that AutoloadGenerator::generateAutoload() would check to see if a extension.json exists, and update it if that was the case. Otherwise it'll just update autoload.php if that file exists..