I've managed to build some device ( 2 axis encoder for 2 piezo translation stages in vacuum if you must know, yes arduino made it into physics :-) ) and put in in a nice box. led control library works great, arduino just made my day :-)
But the auto-reset feature, as nice as it is while still working with the code, as soon as the box just has to work kills all the data acquired. I cannot disable the dtr line in my lab software (closed source), so I just had to remove this R2/3 capacitor. Btw. there is no pdf document/image that would show where R2/3 are, had to run eagle to find it :-( I consider myself quite skilled in those things - but it was hell. Removing smd parts without proper tools... hey !
For people who usually just use those nice prototype breadboards this is the perfect way to do permanent damage to the arduino pcb for sure.
so puhlease, put a jumper next to R2/3 to disable the auto reset :-)