Document all the options passed to the `run` command

[bgaillard]

This issue is related to #10.

All the options passed to the run command have to be documented in the README.MD file.

NOTE: Their is a known Windows issue with the --template parameter when the phpDocumentor PHAR file is used. The documentation should indicate that Windows users have to use the system phpdoc command if they want to use the --template parameter. This should be temporary until the issue is fixed by the phpDocumentor team.