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Just a quick note to let folks know that Ionic has been updated - both the framework (the UI and UX bits, basically what you see) as well as the CLI itself. This forum post details the changes in the Ionic framework itself: http://forum.ionicframework.com/t/v1-0-0-beta-12-krypton-koala-released/9435.
As for the CLI, I'm not aware of a document just for that, but the latest version is 1.2.4 and a cool new addition has landed. You can now seed an Ionic project with the contents of a directory. This joins the existing other options (one of the three main templates or a CodePen) and is a great addition. Personally I think the "blank" template is perfect (and wish the Cordova default project was as good), but I know I'm going to need to tweak it a bit and once I do, I'll create a copy and use it for future Ionic projects.
In honor of this release - here is a result from a Google image search for "krypton koala":
Image credit: Discovery News