Alison Gianotto has an article posted to her since basically answering the "now what?" question resulting from you running Composer as root on your system.

Composer is a PHP dependency manager that’s used in just about any modern PHP application, and it works similarly to how Bundler works for Ruby.

Even though Composer itself gives you a warning about not running it as root, lots of people disregard this warning and run it as root anyway. We run into this issue a lot on my open source asset management project, Snipe-IT, so I figured I’d write up how to fix this if you inadvertently (or advertently) ran composer as root.

She starts by describing the difference between "installing Composer as root" and "running the Composer install as root" (two very different things). She points out that, while Composer tries to prevent the second but permissions errors sometimes cause people to move forward as root anyway, despite the warning. She then shows how to fix the permissions issues so it can be run as a normal user, updating the files in .composer for the root account and re-running the install.