Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:
* added program options to pdbdistance-vineyard
* pdbdistance-vineyard takes frame list in a file
* more logging
* verification of pairing after vertex transpositions (commented out)
/*
* 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
*/