The IDE does it via hardware as well that's why the older model arduinos don't support just hitting the upload button. There is lots of documentation for retrofitting the "auto-reset" functionality on older model arduinos but I didn't see anything about the signal the IDE sends to tell it to reset 
The problem i have is that the firmware seems to become corrupted after a while so it's pretty important that it can be done from the host machine. I might just replace the chip and hope it was a lemon but if I can do it from the host machine I won't have to replace it just yet and I can get it working now instead of when I'm able to get to it next.
Edit: so far as i can tell the board was borked. when i got back to it i manually reset it and flashed it but it still wan't working so i swapped the chip for a known working one and it still didn't work Lucky I had an Uno on hand ... now I need to fix my code on the host machine so it updates IRC and twitter correctly XD