Apparently, you can override port/board configurations by creating a folder and including the path in the make command:
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make BOARD=myboard BOARD_DIR=~/src/projects/myboard
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GNUmakefile
mpconfigboard.mk
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# Enable/disable extra modules
MICROPY_PY_LWIP ?= 1
# wiznet5k module for ethernet support; valid values are:
# 0 : no Wiznet support
# 5200 : support for W5200 module
# 5500 : support for W5500 module
MICROPY_PY_WIZNET5K ?= 5500
# cc3k module for wifi support
MICROPY_PY_CC3K ?= 0
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include Makefile
CFLAGS += -Wno-error
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make: *** No rule to make target 'build-PYBD_SF2/genhdr/pins.h', needed by 'build-PYBD_SF2/py/mpstate.o'. Stop.
I don't think this is very user friendly, as it means that you have to first copy the original file, and then modify it which will lead to problems when the original file is modified at source, or am I not doing this right ??