Modified Arduino.mk to use correct upload protocol if not overrided.

The previous comment of upload protocol not working cannot be verified on
linux. If this problem persists on cygwin, please override with
UPLOAD_PROTOCOL=arduino in the enivornment before calling Arduino.mk

libraries/AP_Common/Arduino.mk

@@ -325,10 +325,9 @@ MCU			:=	$(shell grep $(BOARD).build.mcu $(BOARDFILE) | cut -d = -f 2)
 F_CPU			:=	$(shell grep $(BOARD).build.f_cpu $(BOARDFILE) | cut -d = -f 2)
 HARDWARE_CORE		:=	$(shell grep $(BOARD).build.core $(BOARDFILE) | cut -d = -f 2)
 UPLOAD_SPEED		:=	$(shell grep $(BOARD).upload.speed $(BOARDFILE) | cut -d = -f 2)
-# This simply does not work, so hardcode it to the correct value
-#UPLOAD_PROTOCOL		:=	$(shell grep $(BOARD).upload.protocol $(BOARDFILE) | cut -d = -f 2)
+
 ifeq ($(UPLOAD_PROTOCOL),)
-	UPLOAD_PROTOCOL		:=	arduino
+UPLOAD_PROTOCOL		:=	$(shell grep $(BOARD).upload.protocol $(BOARDFILE) | cut -d = -f 2)
 endif
 
 ifeq ($(MCU),)