I am in the process of writing an arduino programmer entirely in javascript using google chrome’s serial API. I am fairly sure this is going to work, as I am implementing stk500 from a java implementation I found as an example, referencing the avrdude code along the way.

This coupled with a cloud compiler I am planning will eliminate the need to use the java arduino IDE :). It will also be natively cross platform. It will also easily integrate well with the ARM based platforms that have come out with similar to arduino programming layers.