So, you want to connect low-level peripherals (like blinky-blinky LEDs) to your Raspberry Pi and use Java Embedded technology to program it, do you? You sick foolish masochist. No, just kidding! That's awesome!
You've come to the right place. I'll step you though it.
And, as with many embedded projects, it all begins with hardware. So, the first thing to do is to get acquainted with the GPIO header on your RPi board. A "header" just means a thingy with a bunch of pins sticking up from it where you can connect wires. See the the red box outline in the photo.
Now, there are many ways to connect to that header outlined by the red box in the photo (which the RPi folks call the P1 header). One way is to use a breakout kit like the one at Adafruit. But, we'll just use jumper wires in this example.
So, to connect jumper wires to the header you need a map of where to connect which wire. That's why you need to study the pinout in the photo. That's your map for connecting wires.
But, as with many things in life, it's not all that simple. RPi folks have made things a little tricky. There are two revisions of the P1 header pinout. One for older boards (RPi boards made before Sep 2012), which is called Revision 1.
And, one for those fancy 512MB boards that were shipped after Sep 2012, which is called Revision 2. So, first make sure which board you have: either you have the Model A or B with 128MB or 256MB built before Sep 2012 and you need to look at the pinout for Rev. 1, or you have the Model B with 512MB and need to look at Rev. 2.
That's all you need for now.
More to come...
Hinkmond