Fixing GFFparser => GFFParser, adjusting to naming scheme.
Adjustments to naming scheme.
Removing unused code.
Changing Feature to be immutable, adding FeatureBuilder.

Includes tests.
Using @Immutable annotation somewhat more.
Changing some comments.
Marking RNA2GeneIDMapper as final.
Fixing GFFstruct=>GFFStruct to naming scheme.
Updates to .gitignore.