Protocol Update: Part 1 -- Enhancements and Bugfixes (No added features)

This merge updates the Message Director, State Server, and Database Server protocol.  
Documentation, Unittests, and actual Implementation have been updated.  
Additionally, there are a number of small architectural changes.  

Please spend a good amount of time reviewing all of the changes... (there are many).

Additionally, please make sure it compiles, without errors, and the following unittests pass on everyone's machines:
 - test_messagedirector
 - test_stateserver
 - test_dbstateserver_yaml

Closes issue: https://github.com/Astron/Astron/issues/89