The purpose of this guide is to help people in setting up their Raspberry Pi - NyboardV0 as a stand-alone unit for programming and controlling Nybble. With the described steps you will end up with a setup that doesn't need any external connections (apart from WiFi connection to the Raspberry Pi).
The steps will go through setting up a vanilla Raspberry Pi (RPi 3A+, 3B+ and Zero W have been tested). The intention is not to describe how to setup a hardened extremely secure solution, that's a scope of many other instructions throughout the internet. Also, the only important modification to Arduino IDE / avrdude is the installation of the autoreset function. If you have already setup your system then you can just read through steps #42-#49 and you should be good to go without the external FTDI module.
As for the physical hardware change you need to connect one of the GPIO pins of your Raspberry Pi to the NyBoardV0 FTDI connector's DTR pin. I have used GPIO 17 pin (physical pin 11) by soldering a connector to the back side of the RPi. You can then connect this connector (pin 11 / GPIO 17) to the FTDI socket DTR pin on NyboardV0 board.
So here goes the steps (again you can skip to steps #42-#49 if you just need the RPi - Arduino programming addition):
3) Write Raspbian Strecth to an SD disk using Etcher
4) Create file "wpa_supplicant.conf" to the root of the SD card (called 'boot' partition) with the following contents (change the country to match your country code and add multiple network sections if you have multiple Wifi SSIDs as in the example):
Note! autoreset already has the default DTR reset pin set at (physical) pin 11, which I've used also. You can change it if you want/need.
45) sudo cp avrdude-autoreset /usr/bin/
46) cd ~/Petoi/arduino-1.8.8/hardware/tools/avr/bin
47) sudo cp avrdude /usr/bin/avrdude-original
48) mv avrdude avrdude-ORIGINAL
49) ln -s /usr/bin/avrdude-autoreset ./avrdude
All done! Now you can use Arduino IDE as you would use it with the external FTDI module. "autoreset" script takes care of sending the proper DTR signal at the proper time through RPi GPIO 17 (physical pin 11), which you wire to NybbleV0 board's FTDI socket's DTR pin.