Although the documentation is not there yet, there are several threads about this in the Umbraco forum, e.g.
http://our.umbraco.org/forum/developers/extending-umbraco/42240-Custom-Tree-in-Umbraco-6
And a reasonable article here:
http://www.theoutfield.net/blog/2012/07/creating-custom-applications-and-trees-in-umbraco-48plus