I have an Atmel SAM4S Xplained Pro, which I program and debug via a USB cable and Atmel's on-board EDBG chip (in other words, the way God intended). At the moment, if I "Stop Debugging" through Atmel Studio (v7.0), the code seemingly continues running (because I continue to get output in the terminal, which is application specific output).
Does anyone know how to stop this from happening, i.e., how to make "Stop" mean "Stop"? It's doing my head in!
Having contacted Atmel, the answer is that the debugger does not hold the MCU reset after debugging is stopped, so the code will continue to run. This is a known issue and is on their backlog to resolve.