Improve doxygen documentation for the VariantBuilder API

-Add full doxygen for all public API functions
-Improve/consolidate class-level comments

Resolves #322
Merge pull request #372 from broadinstitute/dr_improve_variant_builder_doxygen

Improve doxygen documentation for the VariantBuilder API
Revert "Make CMAKE the default build script"

This reverts commit ffe7d3bccf7fe3854d695f9df451ad46c54b31e5.