Get PHPdoc working with new API level documentation

Per email discussions

Php doc wasn't updating.

Also, some output issues (based on 12 Oct) that I couldn't figure.

1) On the last time it ran @ this URL (http://api.civicrm.org/v3/CiviCRM_APIv3/API_Activity/_api---v3---Activity.php.html#functioncivicrm_api3_activity_create)

activity_create target_contact_id is missing & assignee_contact_id is 'wrong'

'assignee_contact_id' a aa

2) I can't figure out how to make it find examples in subfolders.

3) Lastly - I want to use CRM_Utils_Type::typeToString to determine the datatypes in tools/packages/PhpDocumenter/phpDocumenter/InlineTags.inc :: getfields - noting this here as I wanted to try it when everything else is working.