documentation for command line should be updated for nargs + positional arguments

[multifactorid]

There is a well known issue with python that using nargs + will mess up the calculation of positional arguments. Suggest in the documentation either

1. the optional arguments are shown last, after positionional ones, eg inputfile outputfile --print ALL
2. an example using the -- to 'turn off' nargs eating eg --print ALL -- inputfile outputfile