Refactorizing VCF/Jannovar output code.

Introducing abstract class AnnotatedVariantWriter and adding
implementations for writing VCF and Jannovar output.  This cleans up
the Jannovar class a bit more.
More cleanup of the Jannovar class.

Moving download code into DownloadManager classes.  This allows for
further slimming down of the main driver class and easier understanding
of the code.  Also, it should be easier to add/remove transcript data
sources.

The download manager classes could go into their own module.
Adding serialVersionUID to silence Eclipse.
Adding some comment to AnnotatedVariantWriter.
Adding TODO.
Merge pull request #24 from holtgrewe/feature/main_program_cleanup

More main program refactorization