Modified workflow.R to take settings file as cmd arg

I haven't tested that this will execute the whole script from the command line (as ./workflow.R pecan.xml) but that's the idea. Also, even when running in RStudio, the most common mistake students make in the tutorial is forgetting to pass the settings file explicitly to read.settings. In this case we could just tell them to define that as a variable (rather than run those two lines that read it from cmdArgs) and then run the rest of the script.