Add SkipFlagParsing option to Command

We would like to be able to have command arguments that begin with a dash, but that currently triggers the flag parsing and results in an error that our flag was not defined.

We solved this problem by adding an optional Command option called SkipFlagParsing which, if present, disables all flag parsing and allows "normal" (e.g. non-flag) arguments to begin with a dash.