So more on the Buildbot and command line compiles of the arduino.
After using some code and instructions found here I found that I could compile code (only if the library had been compiled first) however I was unable to upload it to my board.
After lots of looking around for a solution I work out that if I write a wrapper for the arduino's avrdude I could get the correct param's for the upload.
Turns out that the Make file was set for 19200 but the chip wants 57600.
So now to test out the latest version of the Arduino.mk file to see if it builds the library correctly.
UPDATE: once setup Arduino-mk-0.5 works apart from upload which needs the baud rate changed to 57600 for the ATMega328