Fix global options swallowing arguments.

[pocallaghan]

The --skip-root-check and --skip-config options were both defined as
InputOption::VALUE_OPTIONAL. In this situation the option will be
assigned the value of an argument that is directly following it. In the
case of a command this is the command name itself, but this causes every
argument to shift along. Since these options are boolean switches, they
can be changed to InputOption::VALUE_NONE. Closes #521.

[pocallaghan]

It's worth noting that --root-dir is also marked as VALUE_OPTIONAL, this doesn't make a lot of semantic sense, since the whole point of the option is to set a root directory. It would therefore probably make more sense as VALUE_REQUIRED. I didn't include this in the pull request purely because it doesn't really change the behaviour. As required or optional, it will swallow the command argument unless a value is specified.

[cmuench]

Thanks

[cmuench]

@pocallaghan I tested the changes. The solution is to use $input->getParameterOption() to check against a global option.