Feature/mr plugin layer test stable

This is a "snapshot" of the 
````
feature/MRPluginLayerTest
````
branch that is working. As there is still alot of work to do, I have cloned the above branch into this one ("Stable") so that this may be used for testing and evaluation.

Instructions and status details on the working MRPluginLayerTest can be found at the bottom of the readme in the seqware-queryengine-backend folder.