Leonardo auto-reset-and-upload changes for Windows (explanation below)

On Windows COM port changes when board switched between bootloader and sketch.  No way to prevent this so now Windows users have to select the upload port separate from the comm port.  Also, handling of reset into bootloader was broken on Windows.  Would occasionally leave the original COM port completely unusable.  Changed the way this reset is initiated.
Finally, had to add upload.disable.flushing=true flag to boards.txt so IDE wouldn't try to flush the original COM port after it disappeared.

app/src/processing/app/debug/AvrdudeUploader.java

@@ -30,6 +30,7 @@ import processing.app.Base;
 import processing.app.Preferences;
 import processing.app.Serial;
 import processing.app.SerialException;
+import static processing.app.I18n._;
 
 import java.io.*;
 import java.util.*;
@@ -63,36 +64,53 @@ public class AvrdudeUploader extends Uploader  {
       return avrdude(params);
     }
 
-    return uploadViaBootloader(buildPath, className);
+    return uploadViaBootloader(buildPath, className);  
+  }
+  
+  private static String selectLeonardoUploadPort() {
+  	String names[] = Serial.list();
+	String result = (String)JOptionPane.showInputDialog(null, processing.app.I18n.format(_("Please select the Leonardo upload port:")), "Select upload port", JOptionPane.PLAIN_MESSAGE, null, names, 0);
+	return result;	
   }
   
   private boolean uploadViaBootloader(String buildPath, String className)
-  throws RunnerException, SerialException {
+  		throws RunnerException, SerialException {
     Map<String, String> boardPreferences = Base.getBoardPreferences();
     List commandDownloader = new ArrayList();
     String protocol = boardPreferences.get("upload.protocol");
     
     // avrdude wants "stk500v1" to distinguish it from stk500v2
     if (protocol.equals("stk500"))
-      protocol = "stk500v1";
-      
+      protocol = "stk500v1";      
+    
 	// need to do a little dance for Leonardo and derivatives:
 	// open then close the port at the magic baudrate (usually 1200 bps) first to signal to the 
 	// sketch that it should reset into bootloader.  after doing this wait a moment for the 
-	// bootloader to enumerate
+	// bootloader to enumerate.  On Windows, also must deal with the fact that the COM port number
+	// changes from bootloader to sketch.
+	String leonardoUploadPort = null;
 	if (boardPreferences.get("bootloader.path").equals("caterina_LUFA")) {
     	try {
-    		Serial serial = new Serial(Integer.parseInt(boardPreferences.get("upload.speed")));
-    		serial.dispose();
-		    serial = null;
-		    Thread.sleep(8000);
+    		Serial.touchPort(Preferences.get("serial.port"), 1200);
+    		Thread.sleep(8000);
     	} catch (SerialException ex) { 
-    	} catch (InterruptedException ex) { }    	
+    	} catch (InterruptedException ex) { }
+
+		if (Base.isWindows()) {
+			leonardoUploadPort = selectLeonardoUploadPort();
+			if (null == leonardoUploadPort) 
+				return false;
+		}
     }
     
     commandDownloader.add("-c" + protocol);
-    commandDownloader.add(
-      "-P" + (Base.isWindows() ? "\\\\.\\" : "") + Preferences.get("serial.port"));
+    if (null == leonardoUploadPort) {
+	    commandDownloader.add(
+    	  "-P" + (Base.isWindows() ? "\\\\.\\" : "") + Preferences.get("serial.port"));
+    } else {
+	    commandDownloader.add(
+    	  "-P" + (Base.isWindows() ? "\\\\.\\" : "") + leonardoUploadPort);    
+    }
     commandDownloader.add(
       "-b" + Integer.parseInt(boardPreferences.get("upload.speed")));
     commandDownloader.add("-D"); // don't erase

hardware/arduino/boards.txt

@@ -149,7 +149,8 @@ mega.build.variant=mega
 leonardo.name=Arduino Leonardo
 leonardo.upload.protocol=avr109
 leonardo.upload.maximum_size=28672
-leonardo.upload.speed=1200
+leonardo.upload.speed=57600
+leonardo.upload.disable_flushing=true
 leonardo.bootloader.low_fuses=0xde
 leonardo.bootloader.high_fuses=0xd8
 leonardo.bootloader.extended_fuses=0xcb

hardware/arduino/cores/arduino/CDC.cpp

@@ -23,20 +23,6 @@
 #if defined(USBCON)
 #ifdef CDC_ENABLED
 
-void Reboot()
-{
-	USB.detach();
-	cli();
-
-	// Reset the microcontroller to run the bootloader
-	wdt_enable(WDTO_15MS);
-	for (;;);
-}
-
-// Define constants and variables for buffering incoming serial data.  We're
-// using a ring buffer (I think), in which head is the index of the location
-// to which to write the next incoming character and tail is the index of the
-// location from which to read.
 #if (RAMEND < 1000)
 #define SERIAL_BUFFER_SIZE 16
 #else
@@ -114,9 +100,14 @@ bool WEAK CDC_Setup(Setup& setup)
 
 		if (CDC_SET_CONTROL_LINE_STATE == r)
 		{
-			if (0 != _usbLineInfo.lineState && 1200 == _usbLineInfo.dwDTERate)	// auto-reset is triggered when the port, already open at 1200 bps, is closed
-				Reboot();
 			_usbLineInfo.lineState = setup.wValueL;
+			// auto-reset into the bootloader is triggered when the port, already 
+			// open at 1200 bps, is closed.  this is the signal to start the watchdog
+			// with a relatively long period so it can finish housekeeping tasks
+			// like servicing endpoints before the sketch ends
+			if (0 != _usbLineInfo.lineState && 1200 == _usbLineInfo.dwDTERate) {	
+				wdt_enable(WDTO_2S);
+			}
 			return true;
 		}
 	}