Raspberry Pi Stand-Alone Programmer
QCPete 
First Attempt - Chip to Chip Programming
My first approach was to use another AVR chip to do the programming. It had been done before by a few others, and documented quite well.
This is what I came across first:
I found that for some of our combined hex files, this wasn't going to fit in the flash. Also, the process to get the hex data into an array and into the compiled code that lives on the programmer was a bit tedious. Either way, I jumped into this rabbit hole, and thought this was going to be the solution for RedBoard Programming. This was the twelve-at-a-time beast that I came up with:
My 12-at-a-time Redboard programming jig is 99% done. I can't wait to send it into the wild tomorrow morning! pic.twitter.com/2BkhlOFp3p
— QCPete (@qcpete) October 14, 2015
Wow, crazy to think that was October 2015. Yikes, time has flown!
After some detailed production yield tracking, we ultimately decided that we still needed to test the boards individually, and so we found that this programmer didn't give us any reductions in labor costs. A bit of a let down, but it also proved that this method of programming was too unreliable. After running a few thousand boards through this thing, we found that boards would often fail at programming on first attempt. Not acceptable for production use. A bit of a bummer, but hey you can't be afraid to fail, and we learned a ton! It was also a great excuse to really try out our Actobotics line of products.