Rhizome is designed basically according to the PAC (Presentation-Abstraction-Control) design pattern. PAC is similar to MVC, but probably better for web development, and definitely better for Rhizome's goals.
The presentation layer bundled with Rhizome, which makes use of Velocity, is not terribly impressive. It does what a presentation layer ought to do, and no more. It is responsible for taking data and formatting it for return to the user.
Rhizome is pretty flexible on the presentation layer. Velocity is included because I like it enough to use it, and don't hate it enough to look for something else. Also, its introspection abilities are excellent, and make template writing much easier. No special interfaces, etc.
Of course, all that it takes to use a different presentation layer is a few lines of code extending from com.technosophos.rhizome.command.AbstractCommand. And a couple of lines of XML in commands.xml.
But one thing should be noted about the presentation layer as it is: No (non-GUI related) processing is done in the presentation layer. No callbacks to the system are used, and no new resources are retrieved from the system once template rendering is initiated. In short, presentation is passive. It takes what it's given, and it presents it. That's all.
This is similar to the Model layer in MVC, but in PAC it is the layer responsible for managing the data.
Rhizome has a robust abstraction layer, packaged in com.technosophos.rhizome.repository. This abstraction provides unified methods of accessing data. The current implementation uses a disk-based repository and indexes.
The abstraction engine is broken into three parts: A repository (or database) for storing entire documents, a searcher for finding resources in the repository (usually by search data and metadata), and an indexer. The indexer takes documents and preprocesses them before storing them in the document repository.
Basically, the abstraction layer of Rhizome is a document database (DocumentDB). It is responsible for storage and retrieval of documents.
In some ways, the Rhizome document DB is itself a PAC: The RepositoryManager manages the repository like a controller. The search, indexing, and repository access tools deal directly with data abstraction. And the document representations (in com.technosophos.rhizome.document) providing a common format for the app's client -- in this case, Rhizome's controller. Thus, the RepositoryManager retrieves content, makes sure it is in the correct format, and then returns to the RhizomeController. (Is this a valid instance of PAC? Probably. PAC controllers can be chainable.)
This layer is responsible for exerting control over the rest of Rhizome. All requests pass through the controller, and the controller is responsible for passing requests to both the repository (abstraction) and whatever the presentation layer is (Velocity, for example).
The com.technosophos.rhizome.controller tree -- and the RhizomeController object specifically -- handle control of the program. RhizomeController is a Front Controller (Which seems to be a compatible pattern with PAC) that can be chained to another controller. Usually, the external controller is a Servlet.
The controller maps requests (from the external controller or user) to a chain of internal commands that must be run in sequence to fulfill the request.