Unfortunately your template doesn't seem to work for me without quite a few tweaks. I have Arduino 1.0. I've followed all the steps in your guide, but I firstly get an error in Step1.mk "Error: no application found". That's because in Step1.mk ARDUINO_APP = /Applications/Arduino23.app when it should be just Arduino.app.
Upon fixing that, I then get
grep: /Applications/Arduino23.app/Contents/Resources/Java/hardware/arduino/boards.txt: No such file or directory
Sometimes I get an error that the compiler can't locate "pins_arduino.h". Doing the following fixes both errors.
In Step1.mk, change
include $(MAKEFILE_PATH)/Arduino23.mk
to
include $(MAKEFILE_PATH)/Arduino1.mk
Also, inside Arduino1.mk "APP_HEADER = WProgram.h" appears to be wrong, as Arduino 1.0 uses Arduino.h.
APPLICATION_PATH in the same file assumes the Arduino 1.0 is called "Arduino1.app" also. Most people won't have a number in their Arduino app name, it'll just be the default Arduino.app. CORE_LIB_PATH should have a lower case "Arduino" in the path, as it's lower case in the filesystem (in Arduino 1.0 at least). Currently, this won't work on case sensitive filesystems. USER_LIB_PATH should have a lower case "libraries".
If leaving the target on All, an error "/bin/sh: Builds/nil: No such file or directory" occurs. After using other targets, the Builds folder is created so the error goes away. A Builds folder should be in the file template.
main.cpp in the project template should be Arduino.h not WProgram.h. Same in the C++ and Library file templates.
Another thing, why do you force people to enter their name and email address to access the files through Google Docs? Why did you remove everything from GitHub? Makes it rather difficult to see what changes have been made... Don't get me wrong, it's great that you're helping out with your template, just seems you're trying to hide it from everyone!