Changing ExtractSequences at Tim's behest.
Adding a whole swath of new tools.  Please see the usage for each tool for more information.

BaitDesigner, CalculateReadGroupChecksum, CheckTerminatorBlock,
CollectIlluminaBasecallingMetrics, CollectIlluminaLaneMetrics,
CollectJumpingLibraryMetrics, CollectOxoGMetrics,
CollectQualityYieldMetrics, CollectRrbsMetrics, GatherVcfs,
LiftOverIntervalList, ScatterIntervalsByNs, SplitSamByLibrary
adding levenshtein distance and checking for nearest command line name
color scheme
some more tweaks