Reverted the patch by KevinOConnor, as it crashes some versions of avr-gcc and caused linking issues.

Marlin/Makefile

 HARDWARE_VARIANT ?= SanguinoA
 MCU              ?= atmega644
 
-#
-Final OMCA board
+#Final OMCA board
 else ifeq  ($(HARDWARE_MOTHERBOARD),91)
 HARDWARE_VARIANT ?= Sanguino
 MCU              ?= atmega644p
 REMOVE = rm -f
 MV = mv -f
 
-# Tool for testing compiler flags
-cc-option=$(shell if test -z "`$(1) $(2) -S -o /dev/null -xc /dev/null 2>&1`" \
-    ; then echo "$(2)"; else echo "$(3)"; fi ;)
-
 # Place -D or -U options here
 CDEFS    = -DF_CPU=$(F_CPU) ${addprefix -D , $(DEFINES)}
 CXXDEFS  = $(CDEFS)
 endif
 #CEXTRA = -Wa,-adhlns=$(<:.c=.lst)
 
-CFLAGS := $(CDEBUG) $(CDEFS) $(CINCS) -O$(OPT) $(CWARN) $(CEXTRA) $(CTUNING) \
-    $(call cc-option,$(CC),-flto -fwhole-program,)
-CXXFLAGS :=         $(CDEFS) $(CINCS) -O$(OPT) -Wall    $(CEXTRA) $(CTUNING) \
-    $(call cc-option,$(CC),-flto -fwhole-program,)
-#ASFLAGS = -Wa,-adhlns=$(<:.S=.lst),-gstabs 
-LDFLAGS = -lm -Wl,--relax
+CFLAGS := $(CDEBUG) $(CDEFS) $(CINCS) -O$(OPT) $(CWARN) $(CEXTRA) $(CTUNING)
+CXXFLAGS :=         $(CDEFS) $(CINCS) -O$(OPT) -Wall    $(CEXTRA) $(CTUNING)
+#ASFLAGS = -Wa,-adhlns=$(<:.S=.lst),-gstabs
+LDFLAGS = -lm
 
 
 # Programming support using avrdude. Settings and variables.
 	$(NM) -n $< > $@
 
 	# Link: create ELF output file from library.
-$(BUILD_DIR)/$(TARGET).elf: $(BUILD_DIR)/$(TARGET).o
-	$(Pecho) "  CXX   $@"
-	$P $(CC) $(ALL_CXXFLAGS) -Wl,--gc-sections -o $@ -L. $^ $(LDFLAGS)
-
-$(BUILD_DIR)/$(TARGET).o: $(OBJ) Configuration.h
+$(BUILD_DIR)/$(TARGET).elf: $(OBJ) Configuration.h
 	$(Pecho) "  CXX   $@"
-	$P $(CC) $(ALL_CXXFLAGS) -nostdlib -Wl,-r -o $@ $(OBJ)
+	$P $(CC) $(ALL_CXXFLAGS) -Wl,--gc-sections -o $@ -L. $(OBJ) $(LDFLAGS)
 
 $(BUILD_DIR)/%.o: %.c Configuration.h Configuration_adv.h $(MAKEFILE)
 	$(Pecho) "  CC    $<"