Add a --debug flag, like we have in ToolRunner-derived tools

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 128953]
Better reporting of runtime errors

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 128954]
--referenceWindow/-w is now --referenceWindows/-w, taking multiple comma-delimited windows

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 128955]