First Pixhawk Build

First, I am a Pixhawk newbie but tenacious and cautious.

I am attempting my very first build for the Pixhawk for the APMRover2; using Windows 7.
I have installed all of the required tools, etc. and am following the instruction list on: dev.ardupilot.com/wiki/building-px4-with-make/
I have downloaded the 3 main pieces of software from Github.

I have run into a few issues , probably due to my folder names.

  1. My 3 main folders are as unzipped from Github:
    a. G:\Development\ThumperDev\pixgit\ardupilot-master
    b. G:\Development\ThumperDev\pixgit\ PX4Firmware-master
    c. G:\Development\ThumperDev\pixgit\ PX4NuttX-master

  2. Issue: after the required make I got this message:

fatal: Not a git repository (or any of the parent directories): .git
…/mk/configure.mk:2 WARNING – A /g/development/thumperdev /pixgit/ardfupilot-master/config.mk file has been written
…/mk/configure.mk:2: Please edit the file to match your configuration, if you use a different board or port

So, is the fatal really fatal or can I ignore it. I don’t understand its relevance.

Yes, a configure.mk file was written as follows:

Select ‘mega’ for the 1280 APM1, ‘mega2560’ otherwise

BOARD = mega2560

HAL_BOARD determines default HAL target.

HAL_BOARD ?= HAL_BOARD_APM2

The communication port used to communicate with the APM.

PORT = /dev/ttyACM0

uncomment and fill in the path to Arduino if installed in an exotic location

ARDUINO = /path/to/Arduino

PX4Firmware tree: fill in the path to PX4Firmware repository from github.com/diydrones:

PX4_ROOT=…/PX4Firmware

PX4NuttX tree: fill in the path to PX4NuttX repository from github.com/diydrones:

NUTTX_SRC=…/PX4NuttX/nuttx

VRBRAIN Firmware tree:

VRBRAIN_ROOT=…/VRNuttX

VRBRAIN NuttX tree:

VRBRAIN_NUTTX_SRC=…/VRNuttX/NuttX/nuttx

Questions:
What “board” name do I use for the Pixhawk? Is it the cpu name?
What actually is a “HAL board” and in my case what do I call it.
What “port” name do I use? I will be using USB from the PC.
By path to Arduino, is that referring to this: C:\Program Files (x86)\Arduino

I probably can figure out the directory edits for the other folders.
Thanks

Ooops, am I asking too many questions??

If so, please let me know.
Thanks