eliminated "instanceof" checks
remove unused id properties
remove unused Witness#isNear()
remove deprecated token linker
remove deprecated token linker
Simple tokens do not need to know about their position in a witness
readded vertex-pair-based transposition support
the ranking of a variant graph  can serve as a comparator for its vertices
removed unused code
some cleanup and minor tweak
JDK-based logging configuration is sophisticated enough
JDK-based logging configuration is sophisticated enough
OO style for graph traversal; functional style for graph joining
Sugiyama layout for variant graphs