That's done while the boards are already populated, but not de-panelized yet. All boards in the panel are connected to the JTAG bus, that connection will be bro

That's done while the boards are already populated, but not de-panelized yet. All boards in the panel are connected to the JTAG bus, that connection will be broken when you remove them from the panel. JTAG traces run in the "frame" of the panel. So you have a single connector on a panel that you use for flashing firmware and doing boundary testing. Dave Jones @eevblog explains that in one of his videos. I can't remember which one, but I'd start search from this series https://www.youtube.com/watch?v=VXE_dh38HjU https://www.youtube.com/watch?v=VXE_dh38HjU