diff --git a/libraries/AP_Common/Arduino.mk b/libraries/AP_Common/Arduino.mk
index 2ba822df91..9850b11475 100644
--- a/libraries/AP_Common/Arduino.mk
+++ b/libraries/AP_Common/Arduino.mk
@@ -208,6 +208,9 @@ CC			:=	$(call FIND_TOOL,avr-gcc)
 AS			:=	$(call FIND_TOOL,avr-gcc)
 AR			:=	$(call FIND_TOOL,avr-ar)
 LD			:=	$(call FIND_TOOL,avr-gcc)
+GDB			:=	$(call FIND_TOOL,avr-gdb)
+AVRDUDE		:=	$(call FIND_TOOL,avrdude)
+AVARICE		:=	$(call FIND_TOOL,avarice)
 OBJCOPY			:=	$(call FIND_TOOL,avr-objcopy)
 ifeq ($(CXX),)
 $(error ERROR: cannot find the compiler tools anywhere on the path $(TOOLPATH))
@@ -412,12 +415,12 @@ all:	$(SKETCHELF) $(SKETCHEEP) $(SKETCHHEX)
 
 .PHONY: upload
 upload: $(SKETCHHEX)
-	avrdude -c $(UPLOAD_PROTOCOL) -p $(MCU) -P $(PORT) -b$(UPLOAD_SPEED) -U $(SKETCHHEX)
+	$(AVRDUDE) -c $(UPLOAD_PROTOCOL) -p $(MCU) -P $(PORT) -b$(UPLOAD_SPEED) -U $(SKETCHHEX)
 
 configure:
 	$(warning WARNING - A $(SKETCHBOOK)/config.mk file has been written)
 	$(warning Please edit the file to match your system configuration, if you use a different board or port)
-	@echo \# Select 'mega' for the original APM, or 'mega2560' for the V2 APM. > $(SKETCHBOOK)/config.mk
+	@echo \# Select \'mega\' for the original APM, or \'mega2560\' for the V2 APM. > $(SKETCHBOOK)/config.mk
 	@echo BOARD=mega     >> $(SKETCHBOOK)/config.mk
 	@echo \# The communication port used to communicate with the APM. >> $(SKETCHBOOK)/config.mk
 ifneq ($(findstring CYGWIN, $(SYSTYPE)),)
@@ -427,12 +430,16 @@ else
 endif
 
 debug:
-	avarice --mkII --capture --jtag usb :4242 & \
-	gnome-terminal -x avr-gdb $(SKETCHELF) & \
+	$(AVARICE) --mkII --capture --jtag usb :4242 & \
+	gnome-terminal -x $(GDB) $(SKETCHELF) & \
 	echo -e '\n\nat the gdb prompt type "target remote localhost:4242"'
 
 clean:
+ifneq ($(findstring CYGWIN, $(SYSTYPE)),)
+	@del /S $(BUILDROOT)
+else
 	@rm -fr $(BUILDROOT)
+endif
 
 ################################################################################
 # Rules