Intermediate commit while converting to the new architecture * Converted Filtration into StaticPersistence and DynamicPersistenceTrails (both right now work with the underlying std::vector rather than std::list order) * Filtration is now just an auxilliary glue (a map between Complex and Persistence) * Whether chains are vectors or lists can be interchanged * Added PersistenceDiagram with a simple bottleneck_distance() function * Converted triangle, alphashapes3d, and cech-complex examples * Lots of organizational changes (factoring utilities out into containers.h, indirect.h, property-maps.h) * Trying to document along the way with NaturalDocs-type comments

/*
 * Author: Dmitriy Morozov
 * Department of Computer Science, Duke University, 2006--2008
 *
 * For now file exists only to store the main page of the documentation
 */

/** \mainpage
 * Detailed description of Dionysus with references to all the classes, 
 * and code samples goes here.
 */

/**
 * \defgroup topology Topology Classes
 */

/**
 * \defgroup geometry Geometry Classes
 */

/**
 * \defgroup kinetic Kinetic Data Structures Classes
 * \ingroup  geometry
 */