Paths to process should be given via argument

> *Important*: Please review and merge https://github.com/phpDocumentor/phpDocumentor2/pull/1495 first; this PR relies on changes made in that PR

In this change I have added the ability to add files and folders to parse using the arguments of phpDocumentor's run command.

An example where you parse the src folder is:

```
phpdoc run src/
```

Please note that `phpdoc src/` does not work because phpdocumentor will think that you try to execute a command instead that that is an argument.