Beginning transition to protocol version 1
SerialConnection.java:
-SerialConnection buffers each incomming message before handing off to Coordinator
-increased serial transfer speed

Driver.java:
-some methods now marked final.  Eventually drivers will pass a handle to themselves when using coordinator methods.

Coordinator.java:
-waits for local arduino link to become ready before continuing setup process
-sends broadcast query to get a list of all remote modules, waits 6 seconds for responses
-processMessage() records responses to broadcast query, adds responding modules to list
-removed code that added all initialized drivers to remote module list.
More eclipse removal
Code cleanup, more work on serial interface
-moved serial processing back to Coordinator
-added more serial ports to the search list
-cleaned up the code a bit
Code cleaup, more work on serial interface
Coordinator.java:
-removed most code in main loop. Serial processing is now handled seperately
-processMessage now private again
-when a message is received from a remote module that modules name is added to a list of known modules
-cleared up most debugging statements since the code seems stable enough
-fixed bug where the serial connection would not try to reconnect if the cable was unplugged

LedFlash.java, StatefullLed.java:
-fixed a bug where the driver would not terminate

Driver.java:
-fixed a bug where the driver would not terminate

Log.java:
-added beginning support for the built in java logger, disabled until a proper formatter can be written

SerialConnection.java:
-fixed incorrect tag
-lowered serial speed for testing

basic_coordinator.ino:
-lowered serial speed for testing
Starting work on Xbee api mode
-added a few new arduino sketches to test transmitting in api mode

api_receive_testing.ino:
-reception works (tested with crafted packets), transmission back to coordinator missing
API transmit mode implemented
-added support for tx in sample remote moduel
-organized arduino sketches by protocol version
Finishing up basic support for application protocol v1
StatefullLed.java:
-changed moduleName to "LOCAL" so it can be used as a testing driver for the local arduino

Coordinator.java:
-removed serialDataAvailable() and broadcastCommand() since neither were needed
-added sendBinaryV0() sendBinaryV1() stubs
-processMessage can now deal with incomming v1 text messages
-passCommand() now checks if the driver is terminated before attempting to pass messages
-prettified the output a bit

SerialConnection.java:
-if a preferred port was given on the command line then don't try to auto-connect to other ports

basic_controller.ino:
-added a sketch to power the local arduino.  Just basic (ugly) code for now.  The stub methods executeCommand() and executeBinary() need to be implemented to control any connected hardware.
Comitting eclipse changes
Major refactoring for transition to protocol 1 (not tested)
Coordinator.java:
-switch from ByteArrayOutputStream to ArrayDeque to store incoming bytes
-marked all protocol 0 methods and variables as deprecated
-sendCommand() and sendBinary() return boolean values indicating success
-major refactoring on the process for reading messages from the USB connection:
  -incomingSerial() blindly writes the data to the byteBuffer
  -message reading moved to the main loop
  -main loop only reads first byte of message, then transfers control to readTextMessage_V1() or readBinMessage_V1() for the rest of the message reading
-added methods to request driver XML data

Driver.java:
-drivers can now have commands and binary data queued for processing. The main loop within run() should check for data on each loop.  This should help implement drivers for low power modules later on.  The drivers can terminate after processing their queues and the Coordinator will start them again if more data is received.

LedFlash.java, StatefullLed.java:
-updated to reflect changes in Driver.java
Final commit for experimental transition to protocol v1
Forgot some eclipse files
Merge branch 'origin/experimental'

Conflicts:
	coordinator_eclipse_workspace/Coordinator/src/org/apparatus_templi/Coordinator.java