All right, so I mistakenly removed some files from the root folder in the linino firmware on the Arduino Yún by executing rm -rf / but aborting it with ^C very quickly. I know it is a bummer, but yes I made that mistake. Now it looks like the Arduino Yún is bricked. I cannot connect over wifi and pressing the reset button by the USB ports does not have any effect.
When I connect it now, the ON LED is on, then the WAN goes ON, and the RX goes on, then the RX goes off, the WAN goes off, the RX goes on, and then the RX goes off. The ON LED stays on all the time, and nothing happens next.
I tried the following the procedure that noblepepper mentions here http://forum.arduino.cc/index.php/topic,199366.0.html which is the following http://forum.arduino.cc/index.php?PHPSESSID=p02505p9ofipp0q71gns50vm06&topic=195589.msg1444249#msg1444249
And does not work for me. The YunSerialTerminal sketch is uploaded successfully over USB (on the micro-USB port) through the Arduino IDE 1.5.5 (LED L13 and a blinking sequence for LEDs RX and TX happens; then, the ON LED remains on). After that, if I open the Serial Monitor, set the speed to 115200 bauds, I can interact with the Arduino Yun. For example, if I write ~1, it replies to me with "Speed set to 115200". If I write ~~, it replies back with "Sending bridge's shutdown command". But I cannot progress from there.
After that, if I try to press the reset button by the USB ports for more than 1 minute and nothing happens.
I was hoping I could restore to factory defaults / upload a firmware / bootloader.. really appreciate your help.