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)
add_subdirectory (alphashapes)
#add_subdirectory (ar-vineyard)
add_subdirectory (cech-complex)
add_subdirectory (consistency)
add_subdirectory (cohomology)
add_subdirectory (fitness)
add_subdirectory (pl-functions)
add_subdirectory (triangle)
add_subdirectory (poincare)
add_subdirectory (rips)