If you follow the manual steps:

cd libtonc-examples/basic/first/source

# Compile first.c to first.o
arm-none-eabi-gcc -mthumb -c first.c

# Link first.o (and standard libs) to first.elf
arm-none-eabi-gcc -specs=gba.specs -mthumb first.o -o first.elf

# Strip to binary-only
arm-none-eabi-objcopy -O binary first.elf first.gba

# Fix header
gbafix first.gba

Then the first project won't build via make anymore:

$ make
linking cartridge
/opt/devkitpro/devkitARM/bin/../lib/gcc/arm-none-eabi/13.1.0/../../../
../arm-none-eabi/bin/ld: cannot find first.o: No such file or directory

The presence of a .o file in the source directory seems to mess things up... We should instead tell people to copy first.c into a new location.