So you never see any text in the black area at the bottom of the IDE? Whether you run from the terminal or not?
Correct - there are never any characters displayed in the black window at the bottom if the IDE. If I run the IDE as a GUI by simply clicking on it and then on "Run" the only thing I see on the screen is the IDE.
I can upload a program to the Arduino board and run it via the IDE, but there is never any information displayed in IDE Serial Monitor during the upload or after turning on the Serial Monitor.. I know the app is actually running by looking at the blinking LED on pin 13 which is being turned on and off by the app.
I can also start the IDE by clicking on it and then on "Run in Terminal". Now when I turn on the Serial Monitor, the data returned by the app on the Arduino board starts flowing in the terminal window that was used to call the IDE, but not in the IDE Serial Monitor window.