Picard genotype concordance

A new command is available as of Picard 1.122 to compare two VCF files for the purpose of genotype concordance.

This PR includes the gmt wrapper with tests to run GenotypeConcordance using Picard 1.123.  @iferguson90 is currently working on the packaging of the latest version of PIcard.

This PR also contains a new RefAlign command intended to replace CompareSnpsSummary for new models that use mpileup.  Currently those CompareSnp results are all zeros since it doesn't handle the new file format.  The new command is entirely VCF based.
Code review. ;-)

I think you should try `Command::V2`.  `Command::V2` was forked from `Genome::Command::Base` and never cleaned up.  The one feature `Genome::Command::Base` has is aiding in indirect resolution of objects.  For example, in `Command::V2` the `build` property can only be resolved by an ID, name, or BoolExpr that matches its data_type, `Genome::Model::Build::ReferenceAlignment`, whereas with `Genome::Command::Base` if it fails to find one of those it will then try to find related objects as an intermediary, e.g. the builds of an `Genome::Model::ReferenceAlignment`.  And with dot syntax the value of `Genome::Command::Base` is usually minimal.