Chief architect of Rancher here. Rancher.io is in fact completely open source. The intention is that Rancher will run below Docker. Rancher currently wraps Docker but going forward that will no longer be the case. We very much want users to use the native Docker CLI and remote API.

Rancher is packaged as a set of Docker containers. This may seem like inception but we build off of the portability guarantees provided by Docker. This means that the storage and networking services we provide should run anywhere Docker runs.

The source code for this project is mostly in https://github.com/rancherio/cattle at the moment. We will be moving things around quite a bit and in the end we will have a lot of repos that comprise the project. https://github.com/rancherio/rancher serves as a meta-repo that packages up all of the other repos.