Adding an 'args' parameter to the plugin framework.

PluginExecutor now takes a plugin_args argument, whose value is now passed through as
an argument to the 'run' method of ADAMPlugin.

Added a new example (test) plugin, TakeNPlugin, which shows a simple use of this parameter.
Merge pull request #258 from genomebridge/plugin-args

Adding an 'args' parameter to the plugin framework.
.gitignore should _not_ ignore .vcf files
ADAMFlatGenotype is a smaller, flat, simpler version of a genotype schema.

Also:
1. Added support for missing genotypes in the VCFLineConverter for ADAMFlatGenotype.
2. Added a ReferenceMapping for the ADAMFlatGenotype
3. the flat genotype converter uses multiple writers for smaller output files.
Changed the argument 'bamFile' to 'vcfFile' in Vcf2FlatGenotype
Added comments to Vcf2FlatGenotype

Also, removed some extraneous imports.