Changed mongovariant package names to new htsjdk and GATK names.

- net.sf.samtools -> htsjdk.samtools
- org.broad.tribble -> htsjdk.tribble
- org.broadinstitute.variant -> htsjdk.variant
- org.broadinstitute.sting.gatk.walkers -> org.broadinstitute.gatk.tools

Restored MongoVCFVariant from 9d4e30b6c250e7ab63227467ae5116c57e7c0d1c^, with updates to gatk package names.