So far I haven't been successful in finding the code, I've found the thread where Hydrazine talks about his results:
http://www.raspberrypi.org/phpBB3/viewtopic.php?t=5269&p=70994
The last picture shows the setup reasonably well, as well as some thanks to me displayed on the screen. I remember he used an Atmel AVR ATMega88. Sadly it seems I have lost the logs of the conversation I had with him while I was at uni, I'll try again at another time to find it as I remember paste bin was used to share code of the AT Mega, not sure about the code for the RPi.
While it's not quite how you envisaged it, I do remember that someone used the RPi as an AVR programmer, although in this instance, it's done with bitbanging.
http://hackaday.com/2012/08/20/raspberry-pi-as-an-avr-programmer/
I don't think it would be too much of a stretch to swap it over to using the SPI port instead (could still bit bang it if needed, not an ideal solution though).
The UART is still there and I know some people use it instead of ssh or a monitor to check what happens during bootup. The debugging messages can be disabled relatively easily though so the use of the UART port could be only for RPi-Micro communication. There is more information here, but the baud is 115200.
http://elinux.org/RPi_Serial_Connection
You could possible use your Maple to connect to the USART port and forward the messages onto the USB if needed.
You can find out the pinout of the GPIO header here, although if you hook up stuff, make sure you hook it up correctly!
http://elinux.org/RPi_Low-level_peripherals
Using something like a Pi Cobbler or a Pi Crust is probably recommended, but initially I just used prototyping wires.
You made me instantly think of this thread:
http://forums.leaflabs.com/topic.php?id=9201
I did feurig's suggestion and came up with this:
Known ARM CPUs (for use with the -mcpu= and -mtune= options):
cortex-m0, cortex-m1, cortex-m3, cortex-m4, cortex-r4f, cortex-r4,
cortex-a15, cortex-a9, cortex-a8, cortex-a5, arm1156t2f-s, arm1156t2-s,
mpcore, mpcorenovfp, arm1176jzf-s, arm1176jz-s, arm1136jf-s, arm1136j-s,
arm1026ej-s, arm926ej-s, fa726te, fmp626, fa626te, fa606te, iwmmxt2, iwmmxt,
xscale, arm1022e, arm1020e, arm10e, arm968e-s, arm966e-s, arm946e-s, arm9e,
arm1020t, arm10tdmi, ep9312, arm940t, arm922t, arm920t, arm920, arm9tdmi,
arm9, arm740t, arm720t, arm710t, arm7tdmi-s, arm7tdmi, fa626, fa526,
strongarm1110, strongarm1100, strongarm110, strongarm, arm810, arm8,
arm7dmi, arm7dm, arm7m, arm7500fe, arm7500, arm7100, arm710c, arm720,
arm710, arm700i, arm700, arm70, arm7di, arm7d, arm7, arm620, arm610, arm600,
arm60, arm6, arm3, arm250, arm2
From reading the thread again, it looks like it's possible to compile for the maple, so it shouldn't be a stretch to do the same for the Cortex-M0. So technically, it's possible to do it, I just haven't tried personally. Maybe when I try to do a sketch for the F0Discovery, I should see if I can compile it on the RPi. If I do that, I'll let you know how it goes. Regarding the python script, that was exactly my sort of thinking.
I believe it would be possible to do that, however I haven't looked at the SWD spec myself. Either way, having the ability to have not only a compact hardware development environment be good, but just generally having debug support for additional projects on the RPi be a great addition. For me, additional pins being used on the RPi isn't a huge hassle as usually there is a large gain in external pins that can be used, but I do know where you're coming from in that sense.
I didn't actually know that the F3 could do 5msps, that's quite impressive, I looked up and it's possible to do dual-sampling as well (ADC 1&2 are paired as is ADC 3&4, so it might be possible to trigger all 4 in close succession). Plus if resolution is not what is needed, you can bump up the sampling speed to 6.25msps (page 200 RM0316). I do plan to get a F3discovery in the future, just for the moment, I can't afford and other projects currently are more important to me at this time.