Plugin doc integration

[cmnbroad]

The doc gen code (DefaultDocWorkUnitHandler.addDefaultPlugins) populates the freemarker map with a nested map named using the value from the returned by the plugin's getDisplayName method, and adds name and file entries for each default instance retuned from the plugin's getDefautlnstances method. This needs to be generalized:

• the method getDisplayName has a misleading name, since its actually used as a property name, which in turn needs to be a valid freemarker variable name (i.e., read-filter isn't valid)
• plugins arg values are not necessarily@DocumentedFeature annotated, so they won't necessarily have a corresponding help file name
• the current system works for GATK read filters, but the GATK annotation plugin has separate default annotations and annotation groups. this may need to be extended to accommodate that case.