5a2v0:
I found this string in the board.txt file
yun.bootloader.file=caterina/Caterina-Yun.hex
This is where the IDE will reference the bootloader file (relative to the folder that holds boards.txt.) You will want to update that file, with your new image, or give your new image a different name and update boards.txt to point to it (probably the safer option.)
then I searched for this file into Yun trought Putty and I found it in: /etc/arduino
So if I edit the bootloader's source file, compile it and replace the file on Yun, if I upload sketches on my yun over WiFi with IDE, my Yun get the new one and I solve the problem right ?
To be correct, you need to upload your sketch over the network (WiFi or wired Ethernet) and it will update the bootloader on the board. So much of the Yun documentation only mentions WiFi: in reality the Yun is a fully functional router with both wired and wireless networking, and all of the communications/programming options work equally well over either interface.
Or this files is used only for upload trought the yun's web interface?
That file is definitely used for loading code through the IDE over the network, and it should also be used by the web interface. You can also manually put your sketch's hex file on the Yun's disk system and run the programming sequence manually:
merge-sketch-with-bootloader.lua path_to_sketch.hex
run-avrdude path_to_sketch.hex
Note that /usr/bin/merge-sketch-with-bootloader.lua references /etc/arduino/Caterina-Yun.hex internally. If you give your updated bootloader a new name (which I think is a good idea) then you will have to update this reference as well.
When you upload code through the USB port using the IDE, you are going through the Yun's bootloader. If you upload it over the network (either using the IDE, the web interface, or by manual commands using SSH) you are first combining the sketch with the bootloader into a combined image, and then running avrdude on the Linux processor. avrdude then acts like an ICSP programmer, and will completely reprogram the AVR processor using the combined bootloader and sketch image. So yes, programming over the network will indeed update the bootloader image in the Yun's AVR processor.
But, where can i found the Yun's bootloader source file?
It looks like the source and makefile are in the bootloader\caterina folder that is below the folder that holds boards.txt.