We're in the process of making the Arduino IDE support the Wiring board. Soon, you'll be able to pick "Arduino" or "Wiring" in the IDE and then compile and upload your program for that board. The files in lib/targets/wiring are the Wiring libraries, but most are specific to the Wiring board's atmega128 and won't work on the Arduino board. We're also trying to port those libraries for use with the Arduino board.