Makefile: ignore file in automatically generated dependencies

Question

I have the following makefile, (mostly) generated by STM32CubeMX and slightly modified:

##########################################################################################################################
# File automatically-generated by tool: [projectgenerator] version: [3.16.0] date: [Mon Jun 06 11:00:27 SGT 2022]
##########################################################################################################################

# ------------------------------------------------
# Generic Makefile (based on gcc)
#
# ChangeLog :
#   2017-02-10 - Several enhancements + project update mode
#   2015-07-22 - first version
# ------------------------------------------------

######################################
# target
######################################
TARGET := mytarget

######################################
# building variables
######################################
# debug build?
DEBUG := 1
# optimization
OPT := -Og

#######################################
# paths
#######################################
# Build path
BUILD_DIR := build

######################################
# source
######################################
# Generated directories
CORE_SOURCES := $(filter-out Core/Src/main.c,$(wildcard Core/**/*.c))
DRIVER_SOURCES := $(wildcard Drivers/STM32WBxx_HAL_Driver/**/*.c)
C_SOURCES := $(CORE_SOURCES) $(DRIVER_SOURCES)

# ASM sources
ASM_SOURCES := startup_stm32wb55xx_cm4.s

# C++ sources
CXX_SOURCES := $(wildcard App/**/*.cpp App/*.cpp)

#######################################
# binaries
#######################################
PREFIX := arm-none-eabi-
# The gcc compiler bin path can be either defined in make command via GCC_PATH variable (> make GCC_PATH=xxx)
# either it can be added to the PATH environment variable.
ifdef GCC_PATH
CC  := $(GCC_PATH)/$(PREFIX)gcc
CXX := $(GCC_PATH)/$(PREFIX)g++
AS  := $(GCC_PATH)/$(PREFIX)gcc -x assembler-with-cpp
CP  := $(GCC_PATH)/$(PREFIX)objcopy
SZ  := $(GCC_PATH)/$(PREFIX)size
else
CC  := $(PREFIX)gcc
CXX := $(PREFIX)g++
AS  := $(PREFIX)gcc -x assembler-with-cpp
CP  := $(PREFIX)objcopy
SZ  := $(PREFIX)size
endif
HEX := $(CP) -O ihex
BIN := $(CP) -O binary -S
 
#######################################
# CFLAGS
#######################################
# cpu
CPU := -mcpu=cortex-m4

# fpu
FPU := -mfpu=fpv4-sp-d16

# float-abi
FLOAT-ABI := -mfloat-abi=hard

# mcu
MCU := $(CPU) -mthumb $(FPU) $(FLOAT-ABI)

# macros for gcc
# AS defines
AS_DEFS :=

# C defines
C_DEFS :=  \
-DUSE_HAL_DRIVER \
-DSTM32WB55xx


# AS includes
AS_INCLUDES :=

# C includes
C_INCLUDES :=  \
-isystem Core/Inc \
-isystem Drivers/STM32WBxx_HAL_Driver/Inc \
-isystem Drivers/STM32WBxx_HAL_Driver/Inc/Legacy \
-isystem Drivers/CMSIS/Device/ST/STM32WBxx/Include \
-isystem Drivers/CMSIS/Include


# compile gcc flags
ASFLAGS := $(MCU) $(AS_DEFS) $(AS_INCLUDES) $(OPT) -Wall -fdata-sections -ffunction-sections

CFLAGS += $(MCU) $(C_DEFS) $(C_INCLUDES) $(OPT) -Wall -fdata-sections -ffunction-sections
CXXFLAGS += $(MCU) $(C_DEFS) $(C_INCLUDES) $(OPT) -fdata-sections -ffunction-sections -std=c++2a -Wall -Wextra -Wpedantic -Werror
MAKEFLAGS += --jobs=12

ifeq ($(DEBUG), 1)
CFLAGS += -g -gdwarf-2
CXXFLAGS += -g -gdwarf-2
endif

# Generate dependency information
CFLAGS += -MMD -MP -MF"$(@:%.o=%.d)"
CXXFLAGS += -MMD -MP -MF"$(@:%.o=%.d)"

#######################################
# LDFLAGS
#######################################
# link script
LDSCRIPT := stm32wb55xx_flash_cm4.ld

# libraries
LIBS := -lc -lm -lnosys
LIBDIR :=
LDFLAGS := $(MCU) -specs=nano.specs -T$(LDSCRIPT) $(LIBDIR) $(LIBS) -Wl,-Map=$(BUILD_DIR)/$(TARGET).map,--cref -Wl,--gc-sections

# default action: build all
all: $(BUILD_DIR)/$(TARGET).elf $(BUILD_DIR)/$(TARGET).hex $(BUILD_DIR)/$(TARGET).bin

info: $(info $(VPATH))

#######################################
# build the application
#######################################
# list of C objects
OBJECTS := $(addprefix $(BUILD_DIR)/,$(notdir $(C_SOURCES:.c=.o)))
vpath %.c $(sort $(dir $(C_SOURCES)))
# list of C++ objects
OBJECTS += $(addprefix $(BUILD_DIR)/,$(notdir $(CXX_SOURCES:.cpp=.o)))
vpath %.cpp $(sort $(dir $(CXX_SOURCES)))
# list of ASM program objects
OBJECTS += $(addprefix $(BUILD_DIR)/,$(notdir $(ASM_SOURCES:.s=.o)))
vpath %.s $(sort $(dir $(ASM_SOURCES)))

$(BUILD_DIR)/%.o: %.c Makefile | $(BUILD_DIR)
    $(CC) -c $(CFLAGS) -Wa,-a,-ad,-alms=$(BUILD_DIR)/$(notdir $(<:.c=.lst)) $< -o $@

$(BUILD_DIR)/%.o: %.cpp Makefile | $(BUILD_DIR)
    $(CXX) -c $(CXXFLAGS) -Wa,-a,-ad,-alms=$(BUILD_DIR)/$(notdir $(<:.cpp=.lst)) $< -o $@

$(BUILD_DIR)/%.o: %.s Makefile | $(BUILD_DIR)
    $(AS) -c $(CFLAGS) $< -o $@

$(BUILD_DIR)/$(TARGET).elf: $(OBJECTS) Makefile
    $(CXX) $(OBJECTS) $(LDFLAGS) $(CXXFLAGS) -o $@
    $(SZ) $@

$(BUILD_DIR)/%.hex: $(BUILD_DIR)/%.elf | $(BUILD_DIR)
    $(HEX) $< $@

$(BUILD_DIR)/%.bin: $(BUILD_DIR)/%.elf | $(BUILD_DIR)
    $(BIN) $< $@    
    
$(BUILD_DIR):
    mkdir $@        

#######################################
# clean up
#######################################
clean:
    -rm -rf $(BUILD_DIR)
  
#######################################
# dependencies
#######################################
-include $(wildcard $(BUILD_DIR)/*.d)

# *** EOF ***

Now, the C_SOURCES directory (Core/Src/, etc) contains main.c that I want to ignore (which I have tried to do, with filter-out). I have reimplemented all of it in main.cpp in CXX_SOURCES, i.e. App/Src/, which I want to compile instead.

However, it looks like the automatic dependency generation still finds, compiles and links Core/Src/main.c instead of App/Src/main.cpp. I am very new to makefiles as a whole and am not sure how to handle this. What can I do?