What the title says. I looked into flow control, as that seems like the obvious answer to "what are these extra lines in my UART communication?" But what I'm seeing doesn't really look like flow control, even if we assume that one line is tied to gnd. Also, I didn't see any other data moving across other lines. As far as I can tell, what I'm seeing is a standard UART TX/RX arrangement, except that there's this third line which is controlled (it seems like) by the master.
It looks like it "ticks" (pulses) every time the master finishes sending a byte, and then it also pulses to indicate that the slave is clear to communicate. I've attached some pictures below of traces that I've taken with a logic analyzer. This is this mighty gecko development board driving communication with the smaller mighty gecko module (EFR32MG12).
EDIT: for detail, this is a mighty gecko dev board talking to the mighty gecko chip/module (EFR32MG12). The lines are unlabeled because they're not listed in the schematic of the device that I'm talking to (the gecko), so I basically went around tapping lines while it talked until I found something. I'm assuming that host TX is the top/black line, as it talks first, and that host RX is the second/brown line, as it's clearly another serial comm line. That leaves the red line as the mystery line.
EDIT 2: changed beaglebone black to mighty gecko dev board. Apologies for the confusion.