I was referring to executing k3flasher.bin (the compiled flasher). I managed to execute it on a Live USB Linux Mint 13 MATE using terminal.
However upon following the instructions provided (./k3flasher mx35to2_mmc.bin info) I get an error which I forgot to copy and paste here. I'll get back to you on that.
EDIT: I misspelled mx35to2_mmc.bin. I will try the correct name now. It's 5:30 AM, though and I have lectures in 3 hours
I might follow up tomorrow.
EDIT2: For some reason k3flasher "cannot find device". I do not know how I achieved it the first time. I followed the instructions to the point. Namely: plug usb in kindle;eject; menu>settings>menu>restart; hold down Vol - button. After the above steps, the screen hangs on the kindle logo with the boy under a tree and this message - "Please wait a moment while your Kindle starts up", I got the same response the first time I tried to enter USB downloading mode. When I run k3flasher, the dots trickle in the terminal, but the kindle is not recognised...