update phpmd ruleset to use (subset) of cleancode

fix various minor issues reported by static analysis
remove redundant php closing tag from several more files

plugins/af_comics/af_comics_template.php

@@ -6,9 +6,8 @@ class Af_Comics_Template extends Af_ComicFilter {
 	}
 
 	function process(&$article) {
-		$owner_uid = $article["owner_uid"];
+		//$owner_uid = $article["owner_uid"];
 
 		return false;
 	}
-}
-?>
+}