Turning an Arduino Project Into a Prototype

An anonymous reader writes: Those of us who fiddle with electronics are probably familiar with this scenario: you've just finished assembling a project using your Arduino/Raspberry Pi/whatever, and it works! You'd like to set it up for long-term use, but... it's just a mass of wires and LEDs and switches. Alexis Matelin has written up a brief but handy guide for turning that mess into a self-contained prototype. He goes from planning out your circuit to designing your schematic to making your board, then working on an enclosure and a battery holder. Matelin also links to a variety of resources for the individual steps involved. It's a straightforward guide written for amateurs. Those of you who have experience with building permanent micro-controller projects: what would you add?