SW-66. Close app threads when click system close ('X') button

openVisualizerGui.py --
   OpenVisualizerGui_app: Close thread-based components openTun, RPL,
      and moteProbes.
   OpenVisualizerGui: Remove direct references to
      individual modules, instead reference indirectly through app.
   Also add logging capability.

moteProbe.py -- Add flag variable to stop processing serial comm. Also,
daemonize thread if in simulator mode. Otherwise, moteProbes sometimes
persist.

openTunLinux.py and
openTunWindows.py -- Finish read thread by sending a UDP packet to TUN
interface, which breaks out of blocking read.

RPL.py -- Cancel timer

OpenWindow.py -- Add reference to application so can close from UI
openvisualizer_utils.py -- Add function to print a list of active
   threads.
logging.conf -- Add openVisualizerGui and remove moteProbeSerialThread
Merge pull request #32 from kb2ma/develop_SW-66b

SW-66. Close app threads when click system close ('X') button
SW-66. Refactor OpenTun[Linux|Windows] as subclasses of OpenTun.

Supports the intent of these classes as operating-specific specializations.
Also provide a single implementation of common code, in OpenTun.
Merge pull request #33 from kb2ma/develop_SW-66e

SW-66. Refactor OpenTun[Linux|Windows] as subclasses of OpenTun.
SW-70. Adding set root command to openVisualizerCli. Also refactoring initialization to include simulator initialization.
Simpler parser of CLI options.
Merge branch 'develop' into personalDevelop
Update from Berkeley origin repo