There was and extra "nuttx" dir:
cp: cannot stat '/home/lucas/p/dronecode/PX4/Firmware/build/aerofc-v1_default/NuttX/nuttx/nuttx/.config': No such file or directory
FAILED: NuttX/CMakeFiles/menuconfig
And the board fixup being executed from the wrong working directory:
nuttx-configs/aerofc-v1/nsh/defconfig
fatal: Path 'nuttx-configs/aerofc-v1/nsh/defconfig' does not exist in 'HEAD'