diff --git a/LUFA/Build/lufa.avrdude.in b/LUFA/Build/lufa.avrdude.in
index 9586ae211d..dcffe84f5e 100644
--- a/LUFA/Build/lufa.avrdude.in
+++ b/LUFA/Build/lufa.avrdude.in
@@ -7,7 +7,7 @@
 #
 
 LUFA_BUILD_MODULES        += AVRDUDE
-LUFA_BUILD_TARGETS        += program
+LUFA_BUILD_TARGETS        += program program_ee
 LUFA_BUILD_MANDATORY_VARS += MCU TARGET
 LUFA_BUILD_OPTIONAL_VARS  += AVRDUDE_PROGRAMMER AVRDUDE_PORT AVRDUDE_FLAGS
 
@@ -20,7 +20,10 @@ LUFA_BUILD_OPTIONAL_VARS  += AVRDUDE_PROGRAMMER AVRDUDE_PORT AVRDUDE_FLAGS
 # -----------------------------------------------------------------------------
 # TARGETS:
 #
-#    program                   - Program target with application using avr-dude
+#    program                   - Program target FLASH with application using
+#                                avrdude
+#    program_ee                - Program target EEPROM with application data
+#                                using avrdude
 #
 # MANDATORY PARAMETERS:
 #
@@ -42,11 +45,18 @@ TARGET             ?= $(error Makefile TARGET value not set.)
 # Default values of optionally user-supplied variables
 AVRDUDE_PROGRAMMER ?= jtagicemkii
 AVRDUDE_PORT       ?= usb
-AVRDUDE_FLAGS      ?= -U flash:w:$(TARGET).hex
+AVRDUDE_FLAGS      ?= 
 
 # Output Messages
 MSG_AVRDUDE_CMD     = ' [AVRDUDE] :'
 
+AVRDUDE_FLASH_FLAGS = -U flash:w:$< $(AVRDUDE_FLAGS)
+AVRDUDE_EEP_FLAGS   = -U eeprom:w:$< $(AVRDUDE_FLAGS)
+
 program: $(TARGET).hex
-	@echo $(MSG_AVRDUDE_CMD) Programming device \"$(MCU)\" with settings \"$(AVRDUDE_FLAGS)\" using \"$(AVRDUDE_PROGRAMMER)\" on port \"$(AVRDUDE_PORT)\"
-	avrdude -p $(MCU) -P $(AVRDUDE_PORT) -c $(AVRDUDE_PROGRAMMER) $(AVRDUDE_FLAGS)
+	@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
+	@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)
diff --git a/LUFA/Build/lufa.build.in b/LUFA/Build/lufa.build.in
index e43996d8e7..2cdf667f33 100644
--- a/LUFA/Build/lufa.build.in
+++ b/LUFA/Build/lufa.build.in
@@ -161,15 +161,15 @@ hex: $(TARGET).hex $(TARGET).eep
 lss: $(TARGET).lss
 
 %.o: %.c
-	@echo $(MSG_COMPILE_CMD) Compiling C file \"$^\"
+	@echo $(MSG_COMPILE_CMD) Compiling C file \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(C_FLAGS) -O$(OPTIMIZATION) -std=$(C_STANDARD) $< -o $@
 
 %.o: %.cpp
-	@echo $(MSG_COMPILE_CMD) Compiling C++ file \"$^\"
+	@echo $(MSG_COMPILE_CMD) Compiling C++ file \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(CPP_FLAGS) -O$(OPTIMIZATION) -std=$(CPP_STANDARD) -x c++ $< -o $@
 	
 %.o: %.S
-	@echo $(MSG_COMPILE_CMD) Assembling \"$^\"
+	@echo $(MSG_COMPILE_CMD) Assembling \"$<\"
 	$(CROSS)gcc -c $(CC_FLAGS) $(ASM_FLAGS) -x assembler-with-cpp $< -o $@
 
 .PRECIOUS : $(OBJECT_FILES)
@@ -178,15 +178,15 @@ lss: $(TARGET).lss
 	$(CROSS)gcc $^ $(CC_FLAGS) $(LD_FLAGS) -o $@
 
 %.hex: %.elf
-	@echo $(MSG_OBJCPY_CMD) Extracting HEX file data from \"$@\"
+	@echo $(MSG_OBJCPY_CMD) Extracting HEX file data from \"$<\"
 	$(CROSS)objcopy -O ihex -R .eeprom -R .fuse -R .lock -R .signature $< $@
 
 %.eep: %.elf
-	@echo $(MSG_OBJCPY_CMD) Extracting EEP file data from \"$@\"
+	@echo $(MSG_OBJCPY_CMD) Extracting EEP file data from \"$<\"
 	$(CROSS)objcopy -j .eeprom --set-section-flags=.eeprom="alloc,load" --change-section-lma .eeprom=0 --no-change-warnings -O ihex $< $@ || exit 0
 
 %.lss: %.elf
-	@echo $(MSG_OBJDMP_CMD) Extracting LSS file data from \"$@\"
+	@echo $(MSG_OBJDMP_CMD) Extracting LSS file data from \"$<\"
 	$(CROSS)objdump -h -S -z $< > $@
 
 clean:
diff --git a/LUFA/Build/lufa.doxygen.in b/LUFA/Build/lufa.doxygen.in
index 532bde5bd5..13055fc743 100644
--- a/LUFA/Build/lufa.doxygen.in
+++ b/LUFA/Build/lufa.doxygen.in
@@ -44,9 +44,11 @@ DOXYGEN_OVERRIDE_PARAMS ?= QUIET=YES
 MSG_DOXYGEN_CMD          = ' [DOXYGEN] :'
 
 # Determine Doxygen invocation command
-DOXYGEN_CMD = ( cat Doxygen.conf ; $(DOXYGEN_OVERRIDE_PARAMS:%=echo "%";)) | doxygen -
+BASE_DOXYGEN_CMD = ( cat Doxygen.conf ; $(DOXYGEN_OVERRIDE_PARAMS:%=echo "%") ) | doxygen -
 ifeq ($(DOXYGEN_FAIL_ON_WARNING), Y)
-    DOXYGEN_CMD = if ( ( cat Doxygen.conf $(DOXYGEN_OVERRIDE_PARAMS:%=; echo "%") ) | doxygen - 2>&1 | grep -v "warning: ignoring unsupported tag" ;); then exit 1; fi;
+    DOXYGEN_CMD = if ( $(BASE_DOXYGEN_CMD) 2>&1 | grep -v "warning: ignoring unsupported tag" ;); then exit 1; fi;
+else
+    DOXYGEN_CMD = $(BASE_DOXYGEN_CMD)
 endif
 
 doxygen: