Just posting some ideas I have for the future:
-make the reference window pop up with it's right side aligned with the main window's right side (opinions on this?)
-fix the double clicking in the reference window (use JList's methods for this, I found them after I had written my own code for it that I don't think works as well)
-fix whatever is wrong so that the program often starts without enough room to display the JTextAreas which makes it look dumb until you proceed to another verse/challenge pair.
-fix/write the whole help manual thing (probably use a cop out that points the person to this site and the README)
-figure out some better stuff for the status label thing. I'm considering a JTextField that is colored like the background so it blends in but is more stable in the layout
-add some sort of save option when closing if there have been changes to journal since the last save (or startup). This means I have to track that somehow...
-make the window resizable with the layout changing properly
-probably need to fix the whole weird static-ness of the LogicCircuit class
So there's a lot of work that needs done. I know this project is inactive, I don't work on it much. I want to change that in the future.