user3219: As stated in www.Arduino.cc FAQ, "Can I use an Arduino board without the Arduino software? Sure. It's just an AVR development board, you can use straight AVR C or C++ (with avr-gcc and avrdude or AVR Studio) to program it."
For UNO/Pro Mini(ATMega328) and ATmega2560, does these two chips support JTAG type (some chip manufacturers may use different name) programmer / hardware-based debugger in same manner as the ST-Link/J-Link programmer/debugger where one can load code into the MCU and perform hardware break point and single stepping? Example as in  STM32 development board with ST-LINK programmer / debugger where the chip has built-in debug circuit that communicate with ST-Link.
Many thanks in advance.

user368: The ATmegaXX8 does not support JTAG, but the ATmegaXX0, 'XX1, and 'XX4 do. The 'XX8 (as well as other AVR families) supports debugWIRE, which allows debugging over ISP. You will need one of Atmel's debuggers such as the AVR ONE! or the Atmel-ICE as well as Atmel Studio in order to use it.

3219: <p>As stated in <a href="http://arduino.cc/en/Main/FAQ" rel="nofollow">www.Arduino.cc FAQ</a>, "Can I use an Arduino board without the Arduino software? Sure. It's just an AVR development board, you can use straight AVR C or C++ (with avr-gcc and avrdude or AVR Studio) to program it."</p>

<p>For UNO/Pro Mini(ATMega328) and ATmega2560, does these two chips support JTAG type (some chip manufacturers may use different name) programmer / hardware-based debugger in same manner as the ST-Link/J-Link programmer/debugger where one can <strong>load code</strong> into the MCU and perform <strong>hardware break point</strong> and single stepping? Example as in  <a href="http://www.st.com/web/catalog/tools/FM116/SC959/SS1532/PF252419?sc=internet/evalboard/product/252419.jsp" rel="nofollow">STM32 development board with ST-LINK programmer / debugger</a> where the chip has built-in debug circuit that communicate with ST-Link.</p>

<p>Many thanks in advance.</p>
 368: <p>The ATmegaXX8 does not support JTAG, but the ATmegaXX0, 'XX1, and 'XX4 do. The 'XX8 (as well as other AVR families) supports debugWIRE, which allows debugging over ISP. You will need one of Atmel's debuggers such as the AVR ONE! or the Atmel-ICE as well as Atmel Studio in order to use it.</p>
