> Is there a way that I can take a current project created 
in 
> the GUI version and extract the command line that could 
be 
> used to accomplish the same thing.
> I have a project that works wonderfully in the GUI and I 
> would like to use those same settings without having to 
> figure out the command line options and possbilty messing 
> it up :)

The file hts-cache/doit.log contains the commandline - you 
can generally copy/paste it in a shell window, it should 
work.