Another refactoring to the PCB is required. I haven't ordered it yet, because I knew somethign like this would be required.

Since I'm new to Raspberry Pi, I didn't know that its levels are at 3.3volts, so by directly attaching 5volt Arduino I could damage the thing.

So, I'm going to add level converter circuit to the board luckily it's not huge and required only for RX and TX signals.

Here is an example of how it is being used (it's the one Adafruit has in their store https://www.adafruit.com/products/757)

http://www.deanmao.com/2012/08/10/uploading-sketches-to-the-arduino-on-the-pi/

Looks like same thing is required for ISP programming, although maybe bare Atmega chip can be programmed using 3.3 volts.

This is something I'm going to test.

P.S. Also will try to post a video today about using keyboard attached to the console session in other remotely connected sessions.