These tools are built on the great Arduino Makefile created by Martin Oldfield. For now this only automates the process of creating a new Arduino project to be built from the Command Line, without running the java IDE (although it's presence is still necessary because we need to use some of it's files).
To create a new project called blink just run:
./start_project blink
This will create a directory called blink in the current working directory, and will assume that the arduino IDE files are in the same directory. You can specify the path to the arduino files by running
./start_project -a /path/to/IDE/files blink
or
ARDUINO_DIR=/path/to/IDE/files ./start_project blink
You can also set this permanently by adding
ARDUINO_DIR="/path/to/IDE/files" to your .bashrc.
It should be obvious that you can use the Makefile without this script, and I recommend that you read Martin's blogpost before you start using this tools.