[Ernst Blofeld]

Have you definitely done a clean after modifying your makefile? There aren't any left over .o files anywhere?

When I wanted to add assembly files to my project I found that the gcc assembler was just not useable. I used vasm instead and named the files I wanted it to assemble with a different suffix so that I could create a separate process within the makefile for them. Then you're free to do what you want without breaking any existing stuff.

Edit: I see you need -xassembler-with-cpp. My solution won't work for you if this is the case, unless you can break that into a separate step.

Edit 2: How do you stop it from trying to assemble the generated a.mingw.s file? Also, are you on the latest preview version of the vscode extension?

Edit 3: This works for me, apart from that pesky a.mingw.s, using the latest preview extension. I've added a test.s file with one test function included. Not an exhaustive test, but no errors. I would still recommend adding in vasm instead though.

# to generate assembler listing with LTO, add to LDFLAGS: -Wa,-adhln=$@.listing,--listing-rhs-width=200
# for better annotations add -dA -dP
# to generate assembler source with LTO, add to LDFLAGS: -save-temps=cwd

forward-to-backward = $(subst /,\,$1)

subdirs := $(wildcard */)
VPATH = $(subdirs)
cpp_sources := $(wildcard *.cpp) $(wildcard $(addsuffix *.cpp,$(subdirs)))
cpp_objects := $(addprefix obj/,$(patsubst %.cpp,%.o,$(notdir $(cpp_sources))))
c_sources := $(wildcard *.c) $(wildcard $(addsuffix *.c,$(subdirs)))
c_objects := $(addprefix obj/,$(patsubst %.c,%.o,$(notdir $(c_sources))))
s_sources := $(wildcard *.s) $(wildcard $(addsuffix *.s,$(subdirs)))
s_objects := $(addprefix obj/,$(patsubst %.s,%.o,$(notdir $(s_sources))))
objects := $(cpp_objects) $(c_objects) $(s_objects)

# https://stackoverflow.com/questions/4036191/sources-from-subdirectories-in-makefile/4038459
# http://www.microhowto.info/howto/automatically_generate_makefile_dependencies.html

OUT = a.mingw
CC = m68k-amiga-elf-gcc

CCFLAGS = -g -MP -MMD -m68000 -Ofast -nostdlib -Wextra -Wno-unused-function -Wno-volatile-register-var -fomit-frame-pointer -fno-tree-loop-distribution -flto -fwhole-program -fno-exceptions
ASFLAGS = -Wa,-g,--register-prefix-optional
LDFLAGS = -Wl,--emit-relocs,-Ttext=0,-Map=$(OUT).map

all: $(OUT).exe

$(OUT).exe: $(OUT).elf
	$(info Elf2Hunk $(OUT).exe)
	@elf2hunk $(OUT).elf $(OUT).exe

$(OUT).elf: $(objects)
	$(info Linking a.mingw.elf)
	@$(CC) $(CCFLAGS) $(LDFLAGS) $(objects) -o $@
	@m68k-amiga-elf-objdump --disassemble --no-show-raw-ins --visualize-jumps -S $@ >$(OUT).s 

clean:
	$(info Cleaning...)
	@del /q obj $(OUT).* 2>nul || rmdir obj 2>nul || ver>nul

-include $(objects:.o=.d)

$(cpp_objects) : obj/%.o : %.cpp
	@if not exist "$(call forward-to-backward,$(dir $@))" mkdir $(call forward-to-backward,$(dir $@))
	$(info Compiling $<)
	@$(CC) $(CCFLAGS) -c -o $@ $(CURDIR)/$<

$(c_objects) : obj/%.o : %.c
	@if not exist "$(call forward-to-backward,$(dir $@))" mkdir $(call forward-to-backward,$(dir $@))
	$(info Compiling $<)
	@$(CC) $(CCFLAGS) -c -o $@ $(CURDIR)/$<

$(s_objects): obj/%.o : %.s
	$(info Assembling $<)
	@$(CC) $(CCFLAGS) $(ASFLAGS) -c -o $@ $(CURDIR)/$<

Edit 4: changing the m68k-amiga-elf-objdump line that creates a.mingw.s to create a .txt file instead doesn't seem to break anything.