Can you program a Yun board, through it's Linux FS ?

I'm going to be working on a project where I will be using the Arduino as a mouse. I want a GUI application on my desktop to be able to set speed. It will send a message to the Linux filesystem on the Arduino. Will Linux be able to modify the Main Arduino code to adjust the speed for me?

If the speed of the mouse is a parameter of your sketch (ie: a variable) you can read its value using Bridge.get instead of hardcoding it into the sketch Then, from the linux side (or better with a browser calling a url like http://yun/data/put/speed/10) you can tell the sketch at which speed it should move the mouse