I spent some time over the weekend getting everything figured out. The issue was 3 fold (at least) but I think there may be one issue remaining if I wanted to program the Arduino with HG.
1) permissions
2) GPIO pin
3) board settings
I downloaded the autoreset code from github assuming it was all set up correctly. As it turns out, it was not but I thought I had it covered. The file didn't seem to have execute permissions, so I added that. But, beyond that, it will only work when executed by root. So, I have to run via "sudo make upload". Also, when running via sudo, the pi environment variables are not shared with root. As a result, the "execute BOARD=..." was not accessible from root. I added those statements to my makefile and it was happy again.
Second, the GPIO I was using was the actual GPIO number but the code was set up to use the header pin number. I switched it and it was happy again.
Finally, I had an issue where once I was able to upload, I was not getting a connection to the board over serial. I could upload the blink example with different flash rates correctly, but serial returned garbage. I tried other baud rates with minicom and it turned out that the board was set to 8MHz instead of 16MHz so things were running at double speed. Connecting to the board set to run at 9600 would work if I set minicom to 19200 (2x9600=19200). I deleted the compiled files, updated the BOARD setting, and "sudo make upload".
Now ever thing works as expected! HOWEVER, I have not yet tried with HG. Does HG use "make upload" or "sudo make upload"? If it uses the first, I won't be able to get it to work. I don't plan on changing things on the Arduino once setup, so this is not critical but would be good to know.