software: Fix serial connection issue on OSX/Linux

Turns out that on Ubuntu 14 and OSX El Capitan setting DTR to true
alone does not appear to send the command to the IOIO. Setting it
to false first seems to fix the issue.

software/IOIOBridge/src/main/java/ioio/bridge/Main.java

@@ -148,6 +148,7 @@ private static SerialPort openPort(String portName) {
 				port = (SerialPort) commPort;
 				port.enableReceiveThreshold(1);
 				port.enableReceiveTimeout(500);
+				port.setDTR(false);
 				port.setDTR(true);
 				Thread.sleep(100);
 				return port;

software/IOIODude/src/main/java/ioio/dude/SerialPortIOIOConnection.java

@@ -63,7 +63,9 @@ public void waitForConnect() throws IOException {
 								serialPort_.getInputStream());
 						outputStream_ = serialPort_.getOutputStream();
 
-						// This is only required on Windows, but otherwise harmless.
+						// This is only required on Windows and OSX El Capitan, but otherwise
+						// harmless.
+						serialPort_.setDTR(false);
 						serialPort_.setDTR(true);
 						Thread.sleep(100);
 						return;

software/IOIOLibPC/src/main/java/ioio/lib/pc/SerialPortIOIOConnection.java

@@ -71,7 +71,9 @@ public void waitForConnect() throws ConnectionLostException {
 								1024);
 						outputStream_ = new BufferedOutputStream(serialPort_.getOutputStream(), 256);
 
-						// This is only required on Windows, but otherwise harmless.
+						// This is only required on Windows and OSX El Capitan, but otherwise
+						// harmless.
+						serialPort_.setDTR(false);
 						serialPort_.setDTR(true);
 						Thread.sleep(100);
 						return;