Can you explain the layout of the code?

The bvault code adopts the MVC structure provided by the Zend Framework, with one notable exception. Library classes are kept in ./library, rather than as an ./application/model. This reflects the loosely joined nature of the libraries and the interface, which heavily uses Zend Framework methodology.

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./application
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This is the heart of the MVC framework. The bootstrap.php file is the entry point to the application.

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./html
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This is the htdocs root of the application and holds all the static files (css, js, etc) of the application. The .htaccess file here provides mod_rewrite rules to direct all requests to index.php (except when a file actually exists at that url)

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./library
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There are four distinct libraries that make up the core of bvault: Fedora/, which provides access to the fedora repository APIs (and distributed/federated capabilities); Graph/ offers a force-directed layout library; Vault/ is the core of bVault libraries and provides some classes for Annotations, Tags, Nodes (records), Searching, and Users.

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./tools
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These are some misc. tools built to help with the site. Some of the scripts here are waiting to be refactored into the application or libraries, while others are provided for general interest. Most are directed towards ingest-time use, but some (such as graph/json.php) are actively being used.