What does the green dot blinking in the menu bar mean?
Short answer: A brief green blink of the dot in the menu bar means the Junk Yard just caught something you copied and saved it as a new scrap.
It means the Junk Yard just caught something you copied. A small dot in the menu bar blinks green for a moment each time a new scrap lands, so you know it was saved without having to open the board.
If you copy something and the dot doesn't blink, it wasn't captured — for example because it came from a password manager, it was the same as the last thing you copied, or capturing is switched off. See Why didn't something I copied show up?