Yep, he doesn't seem to have any idea of how a breadboard works. In fact, he's got it completely backwards (LEDs on the power rails and power rails in the component rows). It probably won't blow the ports with the resistors there, but it definitely won't work the way he says it does.
Also, the Arduino IDE already has a serial terminal built in, so all of the Processing terminal handling stuff is moot.
Final point is that running motors from the same supply as the Arduino tends to break down if you put a decent load on them - you'll get brown outs and weird resets.
On the plus side, he does include his bibliography on the last page, so you can check out the original tutorials. That's a pretty decent set of links and books.
I concur, apparently the author forgot how breadboards worked when he fired up Fritzing.
I'm also very confused by the "Arduino IDE" section as the Arduino software includes all dependencies as far as I know.
And "Arduino" doesn't even mean "good friend" ...
The real reason I'm saying this is that his diagrams with the LEDs will not work. The potential across the LED leads is 0. In fact, on the example with 3 chasing LEDs, it may blow the ports (I don't know know if the pin is an open collector or a current source).