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)
#include <utilities/log.h>
#ifdef LOGGING
static rlog::RLogChannel* rlFiltration = DEF_CHANNEL("topology/filtration/info", rlog::Log_Debug);
static rlog::RLogChannel* rlFiltrationDebug = DEF_CHANNEL("topology/filtration/debug", rlog::Log_Debug);
#endif // LOGGING