Transition to protocol 2
MessageCenter.java:
-now a thread to prevent locking buffer
-moved reading messages to run()

Coordinator.java:
-removed all methods for reading messages in protocol 0&1
-added additional code to isModulePresent() to help with string matching (see issue #7)

SerialConnection.java:
-added temporary method flushSerialLine();

basic_controller.ino, led_flash.ino:
-large rewrite of code to support protocol v2.  Code is now much easier to follow and ~2/3 original size.