bug 22891 major secondary documentation refactoring

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 125251]
"rare" is being migrated to a separate package

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 125285]
Tracking bug 22690 - make this a little bit not alarming so I won't be
scared.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 125472]
Better pretty printing of insertions

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 125939]
Diploid quiver functionality

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/GenomicConsensus/": change = 125940]