Back again, but with one step closer. Using 1.5.6r2 instead of 1/0.3 on my Ubuntu box. The IDE sees the /dev/ttyACM0 of the Leonardo. So, I try to upload Blink after changing the blink frequency to know if it works. So, I hit upload, and it compiles and fails to upload without showing an error!
So, I go to preferences and align verbose for the upload attempt. Right at the top of the verboseness is "Forcing reset using 1200bps open/close on port /dev/ttyACMO". The mysterious 1200baud shows up right at the top of the listing. Later down on the listing is where it finds the port, chooses avr109, and shows "Overriding Baud Rate: 57000".
Then it says that the device or resource is busy and thus can't upload to the board. So, how do you prevent it from "force reset using 1200bps open/close on port /dev/ttyACM0"-ing?