Ah, I think more explanation is in order.
Aside from the plugins, the structure of Vesper is just Sinatra, Rack and Rake (/public, /views, config.ru, Gemfile, Rakefile, etc.) plus application and config directories. When the app is run, it does all the normal rackup stuff, and loads everything in /config and /application. There wasn't a need to do anything more.
That's where this whole thing started. I got tired of the routes file in Rails (my biggest Rails complaint), so I switched to Sinatra, and this is how I ended up writing a lot of apps.
Sidenote: /data and /tests are both generated by default plugins.
By unstructured, I just meant the MVC thing. Most frameworks I've used start off with the assumption that I want to use MVC directories. Sometimes I do, sometimes I don't. Most of the time I want to use the concept of models and controllers, but instead of separating them into different directories and files, I want to group related models and controllers together - i.e. a users.rb file with the User class and the associated routes for sign in, profile editing, etc.
The plugins were extracted from code I use in a lot of apps, but not all. That's why a plugin is so similar to a full project, with a few extras thrown in, like hooks (they just run code are certain times during loading). I'm mixed as to polluting the main project with assets, so I just did both. A plugin's /application, gemfile and /tasks don't get moved into the main project. But sometimes it makes sense, such as DataMapper and a /data folder, and MiniTest and a /tests folder. It's really optional.
Now for gems: There's nothing stopping anyone from adding gems to a project. They should work just fine, and I do it all the time. But at the same time, I work with a lot of designers and just-getting-started programmers who have no idea how to write a gem, but still have code they reuse a lot. The 'plugins-as-a-repo-in-a-live-folder' allow for that, while not stopping them from using gems if they fit the bill. A few of the plugins are nothing more than wrappers for gems with a little config pre-written.