Cloud 9 and Eclipse Che are different beasts. The primary difference is around the definition of a workspace. Eclipse Che workspaces have an encapsulation that include their runtimes and a self-hosted IDE. This, then, allows you to run Eclipse Che as a workspace server on any server or desktop. And since the workspaces are defined with configuration files you can move workspaces from one server to another.

The SDK is entirely open source - with no restrictoins, so there is a development model for how to customize both the IDE and the workspace.

Since workspaces embed their own runtimes, you can use Dockerfiles to create completely customized stacks. And we'll be supporting composefiles shortly.

We built Che this way to encourage ISVs to adopt for ucsotmization while also providing a simple IDE for developers. Codenvy uses Che to build out a distributed system that they host at beta.codenvy.com and also is installable by customers behind their firewall.

Cloud 9 is primarily a fully hosted SaaS with their IDE. The IDE features are similar but different, with C9 having more work around collaboration of users within the shared environment.

There is more details beyond this - but this is the essence.