JTAG Debuggers

JTAG: Joint Test Access Group (like JPEG)

It was born as a pcb-testing tool
You could read and write individual pins

It is now mainly a sw debugging tool
You can read and write internal bits as well
You can access machine registers
You can send commands and read results
Clearly, you can still drive pins
You can thus drive external hardware
e.g.you can program your external flash/eeprom

The easiest use case is running a host application
The application talks the gdbserver protocol
... and drives jtag signals using an external tool

OpenOCD works in this way