Numerous updates to Biers to make it compatible with
- RNAstructure v6.0, including fixes to DMS readin to ShapeKnots, bootstrapping, and 2D data readin to ShapeKnots/Fold
- VARNA – remove reliance on web browser JAVA to display VARNA structures, and instead use "command-line" calls to VARNA.jar
- improved utilities for converting dot-parens structure to base pairs and back
- moving some tools in HiTRACE into Biers.
- Directory reorganization by application type (M2seq, SHAPE, DMS, etc.).