Feature/pluginsim

This feature branch contains various changes. Work has been done on:

- Defining what the PluginRunnner will accept as an input specifically.
- Modification of GATK_Picard_BackendTest for nearly complete hooking to the test harness. Along with HTML Report output.
- To be done:
  - Finish the PluginRunner
  - Finish defining what a setting file is, and how it will affect the backend.

I have commented out the Picard/SAMTools portion of the test harness so that it can run with mvn clean install.

Running  ````mvn clean install```` should be able to work. Although it took ~40 minutes to download, decompress, query and build the .jar file. If you wish to shorten this, just comment out the download links in the test harness so that only one is used.