Paths to process should be given via argument

In this change I have added the ability to add files and folders to parse using the
arguments of phpDocumentor's run command.
Merge branch 'feature/add-support-for-multiple-backends' into feature/select-files-and-folders-using-argument
Merge branch 'feature/add-support-for-multiple-backends' into feature/select-files-and-folders-using-argument
Merge pull request #1498 from mvriel/feature/select-files-and-folders-using-argument

Looks good...