Add $(MAKEFILE_LIST) as a dependency on build rules that could be altered by changes to the makefiles - if the user alters the project makefile, require that all modules are rebuilt.

LUFA/Build/lufa.avrdude.in

@@ -53,10 +53,10 @@ MSG_AVRDUDE_CMD    := ' [AVRDUDE] :'
 AVRDUDE_FLASH_FLAGS = -U flash:w:$< $(AVRDUDE_FLAGS)
 AVRDUDE_EEP_FLAGS   = -U eeprom:w:$< $(AVRDUDE_FLAGS)
 
-program: $(TARGET).hex
+program: $(TARGET).hex $(MAKEFILE_LIST)
 	@echo $(MSG_AVRDUDE_CMD) Programming device \"$(MCU)\" with settings \"$(AVRDUDE_FLASH_FLAGS)\" using \"$(AVRDUDE_PROGRAMMER)\" on port \"$(AVRDUDE_PORT)\"
 	avrdude -p $(MCU) -P $(AVRDUDE_PORT) -c $(AVRDUDE_PROGRAMMER) $(AVRDUDE_FLASH_FLAGS)
 
-program-ee: $(TARGET).eep
+program-ee: $(TARGET).eep $(MAKEFILE_LIST)
 	@echo $(MSG_AVRDUDE_CMD) Programming device \"$(MCU)\" with settings \"$(AVRDUDE_EEP_FLAGS)\" using \"$(AVRDUDE_PROGRAMMER)\" on port \"$(AVRDUDE_PORT)\"
 	avrdude -p $(MCU) -P $(AVRDUDE_PORT) -c $(AVRDUDE_PROGRAMMER) $(AVRDUDE_EEP_FLAGS)

LUFA/Build/lufa.build.in

@@ -177,15 +177,15 @@ elf: $(TARGET).elf
 hex: $(TARGET).hex $(TARGET).eep
 lss: $(TARGET).lss
 
-%.o: %.c
+%.o: %.c $(MAKEFILE_LIST)
 	@echo $(MSG_COMPILE_CMD) Compiling C file \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(C_FLAGS) $< -o $@
 
-%.o: %.cpp
+%.o: %.cpp $(MAKEFILE_LIST)
 	@echo $(MSG_COMPILE_CMD) Compiling C++ file \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(CPP_FLAGS) -x c++ $< -o $@
 	
-%.o: %.S
+%.o: %.S $(MAKEFILE_LIST)
 	@echo $(MSG_COMPILE_CMD) Assembling \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(ASM_FLAGS) -x assembler-with-cpp $< -o $@
 

LUFA/Build/lufa.dfu.in

@@ -45,13 +45,13 @@ MSG_COPY_CMD   := ' [CP]      :'
 MSG_REMOVE_CMD := ' [RM]      :'
 MSG_DFU_CMD    := ' [DFU]     :'
 
-flip: $(TARGET).hex
+flip: $(TARGET).hex $(MAKEFILE_LIST)
 	@echo $(MSG_DFU_CMD) Programming FLASH with batchisp using \"$(TARGET).hex\"
 	batchisp -hardware usb -device $(MCU) -operation erase f
 	batchisp -hardware usb -device $(MCU) -operation loadbuffer $(TARGET).hex program
 	batchisp -hardware usb -device $(MCU) -operation start reset 0
 
-flip-ee: $(TARGET).eep
+flip-ee: $(TARGET).eep $(MAKEFILE_LIST)
 	@echo $(MSG_DFU_CMD) Copying EEP file to temporary file \"$(TARGET)eep.hex\"
 	cp $(TARGET).eep $(TARGET)eep.hex
 	@echo $(MSG_DFU_CMD) Programming EEPROM with batchisp using \"$(TARGET).eep\"
@@ -61,13 +61,13 @@ flip-ee: $(TARGET).eep
 	@echo $(MSG_DFU_CMD) Removing temporary file \"$(TARGET)eep.hex\"
 	rm $(TARGET)eep.hex
 	
-dfu: $(TARGET).hex
+dfu: $(TARGET).hex $(MAKEFILE_LIST)
 	@echo $(MSG_DFU_CMD) Programming FLASH with dfu-programmer using \"$(TARGET).hex\"
 	dfu-programmer $(MCU) erase
 	dfu-programmer $(MCU) flash $(TARGET).hex
 	dfu-programmer $(MCU) reset
 
-dfu-ee: $(TARGET).hex $(TARGET).eep
+dfu-ee: $(TARGET).eep $(MAKEFILE_LIST)
 	@echo $(MSG_DFU_CMD) Programming EEPROM with dfu-programmer using \"$(TARGET).eep\"
 	dfu-programmer $(MCU) eeprom-flash $(TARGET).eep
 	dfu-programmer $(MCU) reset