Directly using the Helper classes in AnnotationBulidDispatcher.
Removing intermediate Builder layer.
Renaming BuilderHelper classes to Builder classes
Moving class around.
Fixing command line documentation.
Fixing command line.
Renaming Ensenble to Ensembl.
Handling bad case "CDS starts before TX" for GFF.

This occurs in the case of ENSEMBL.
Fixing correction of ENSEMBL GTF CDS begin/end positions.