Software running onboard the Arduino Mega 2560 Rev3 and the Arduino Micro in flight, within the balloon payload; and also the software on the Arduino Mega 2560 Rev3 within each ground station. Most of the actual code is within C++ classes within the "libraries" subdirectory (just as it should be! <shakes finger...> :) .
On Windows machines, please note that one might additionally have to install the following libraries (each via the Arduino IDE library manager): RadioHead, SdFat, TinyGPSPlus.