In the uploader options, there is the option to use:

Atmel Studio JTAG ICE3 (ISP)

This is favorable as the Atmel Studio built-in programming works more reliable with e.g. the ICE3 programmer. However, when debugging is required, it is necessary to switch the connection to JTAG. However, there is no corresponding programming mode, which might look like:

Atmel Studio JTAG ICE3 (JTAG)

Using "Atmel JTAGICE3 (JTAG mode)" isn't really reliable, and while using "Atmel Studio Device Programming" does work, I need to manually start the upload in the "Device Programming" dialog every time I do a build.

Can you please add an option so that Visual Micro will use the built-in JTAG programming from Atmel Studio in the same way it already works for ISP?

Thank you.

The programmers in the list are the ones provided by arduino.cc and some by a few users.

The best option is to use the "Use Atmel Studio Device Programming" but I need to look into why you feel you have to manually start the upload each time you click "Start>Debug" or "Start>Without Debug".  Is this the issue?

Out of interest, have you got "Debugger>Use atmel studio debugging" enabled?