I pushed the new Organization API documentation today. You can now access and modify Organization and Team information for your repositories.
The Org API managed to test the limits of the current GitHub API. Traditionally, the Repository API actions required only the name to update your repo information. This worked well since most of the repos that you modified were owned by your own user. With Organizations, this is no longer the case, so we deprecated several of the old Repository API actions. You are encouraged (but not required) to pass the user login and the repo name for these actions (check the docs for more details):
repos/delete/:repo repos/set/private/:repo repos/set/public/:repo repos/keys/:repo repos/key/:repo/add repos/key/:repo/remove repos/collaborators/:repo/add/:collaborator repos/collaborators/:repo/remove/:collaborator
Thank you to all the developers that helped us out during the beta. We received some valuable feedback that helped us fine tune the APIs and ensure its consistency. If you are a developer that works with the API a lot, be sure to follow the API Support Forum for announcements on new API updates.