Started back on Documentation

So after a long break (I think May was the last time this was touched) got back into doing the documentation. It probably took a day just to orientate to where we were. Anyhow the main purpose of doing the documentation before the technical work is complete is to pin down the workflow and hence what the commands and options will need to be provided by the wrapper toolkit. This so far has been quite successful in identifying any gaps in the technical implementation (due to the attempt to reflect real use cases).