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)
Write an audit for the data structure.
-DBOOST_UBLAS_TYPE_CHECK=0 is necessary since otherwise Boost's uBLAS gives a compile-time error
when it doesn't find sqrt for polynomials. It doesn't actually need it (e.g., for LU-decomposition,
but it looks for it during type check). (File a bug report with Boost?)