Decouple ParseAndRun to allow customization of Invocation

[cardil]

Fixes #445

I'm introducing two functions Run and HandleParseError which allow users to customize the Invocation after it is parsed.

For example:

inv, cmd, err := Parse(stderr, stdout, args)
if retcode, doExit := HandleParseError(err, stderr); doExit {
  return retcode
}
inv.Stdin = stdin

# example customization
inv.WorkDir = ".." 
inv.Dir = "."

return Run(inv, cmd)