Fixes #1450 - explanation of phpdoc.xml vs phpdoc.dist.xml
Fixed broken reference links

- Fixed broken cross-links to other doc files
- Added a slight bit more clarity to the wording
Incorrect CLI parameter

Fixed incorrect config switch name
 (See
https://github.com/phpDocumentor/phpDocumentor2/blob/develop/src/phpDocu
mentor/Configuration/Loader.php#L71-L78 for verification)
Merge pull request #1454 from drbyte/develop

Fixes #1450 - explanation of phpdoc.xml vs phpdoc.dist.xml