Issue a "reset and halt" command on SWD, before programming

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I just learned that the Flash programming in Atmel Studio (the "Start Without Debugging" and "Start Debugging" buttons) doesn't initially reset the MCU that runs with current configurations during Flash programming.

My target MCU is SAMD20 and I'm trying to change clock (and other) configurations. So I would like to perform the Flash Programming starting from a well-known state, the state after reset.

SWD interface has a reset line and a reset command can be send to the target device before programmin... however Atmel Studio doesn't perform a full reset, only a halt command. Is it possible to change this behaviour so the debugger (in my case J-Link) send a reset before Flash programming?