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.