Updates to CLP documentation in preparation of the single CLP jar
Merge pull request #28 from broadinstitute/jg_branch_nh_single_clp

Updates to CLP documentation in preparation of the single CLP jar
Merge pull request #27 from broadinstitute/gg_branch_nh_single_clp

Slight update to usage information text
Edit CommandLineProgramProperties annotations.
Merge pull request #30 from broadinstitute/aw_single_clp

Edit CommandLineProgramProperties annotations.
Brad's command line usages updates
Merge pull request #32 from broadinstitute/bt_usage_updates

Brad's command line usages updates
Updated usage documentation and programGroup info for single command line program effort.