I would like to be able to debug two RFM69 modules on different ports.
With the previous IDE I was able to start two instances from different workspaces and select the connected ports interdependently. This allowed access to my Tx node RFM registers at the same time as access to my Rx node registers.
With previous versions of the Arduino IDE 2.x, it was possible to use a separate port in each IDE window, without even the need for the multiple instances trick we use with Arduino IDE 1.x to achieve that. Unfortunately, it has not been possible to use multiple ports at the same time effectively with the latest releases of Arduino IDE 2.x due to a regression in the Serial Monitor:
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I think it is reasonable. You might prefer to continue using 1.x as your every day tool for developing sketches while also using 2.x when you want to contribute to the Arduino IDE project by doing beta testing or when you need its unique features such as the language server (e.g., "Go to definition") and the integrated debugger.
The workaround would be to use a separate serial terminal. That could be the Arduino IDE 1.x Serial Monitor, one of the excellent standalone terminals such as PuTTY, screen, or arduino-cli monitor.
Note that if you do this you will need to remember to close the serial port in whichever terminal application you are using before uploading to that board from the Arduino IDE. The integration between the Arduino IDE and its Serial Monitor allows the closing and opening of the port during an upload to be done automagically, but when using a separate terminal it is necessary to do that manually. The port can only be open in one application at a time, so if it is open in the terminal when you try to upload, the process will fail.
Just FYI I ran ~/.arduino15/packages/builtin/tools/serial-discovery/1.3.1/serial-discovery and all was OK with two boards on different ports. Linux Ubuntu 18.04.
I'm glad to hear that serial-discovery is working correctly for you.
This is the tool the Arduino IDE uses to populate the Tools > Port menu and the new board/port selector menu on the button bar. It is not directly involved in the Serial Monitor, but it is very important for the Arduino IDE's functionality.