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
*/