The functioning of the prototype we're going to realize is quite simple. We need an electronic circuit that can detect the infrared light emitted by the remote controller and then generate some impulses that are caught by a special software that can detect and store them into a configuration file in order to be used at later time. Then, by using a special daemon, we can convert a button pressed on the remote controller into a suitable command for our BeagleBone Black.
In this scenario, the hardware we have to realize is very simple. We just need a small circuitry with an infrared-capable photo diode (infrared receiver). On the other hand, the software part is a bit more complicated due to the fact that we first need a kernel driver to reliably detect the message from the remote control, and then a user-level program to record it, a program to recognize which button has been pressed, and a last program to convert such pressures into on and off commands (or whatever...