Update .gitignore
Update seqware-queryengine.xml
Delete JBrowseNCListFeatureWriter.java
Allow plugins to be started with either a Reference or a group of input feature sets
Fix distribution jar
Make MRHBaseRunner give rows separated by SGID
Working refactor allowing reference and multiple feature set, testing using aggregation plugins

Tested on LocalJobRunner, attempting on cluster
Fix up in memory testing
Disable wiidata hbase cluster for web service until we have tests
Add query by FeatureSet tag support to existing FeaturesByAttributes plugin
Get rid of unnecessary seqware commons code for checking permissions
Create plugins that transparently run pre-filtering.

Move filtering support inside MapReduce runners, dogfood existing filter plugins.
Working prototype for launching filtered plugins from the command-line, testing with ICGC aggregation plugins
Update query language documentation
Merge pull request #5 from SeqWare/feature/plugin_interface_refactor

Feature/plugin interface refactor