Index: phase3/includes/parser/Parser.php
===================================================================
--- phase3/includes/parser/Parser.php	(revision 102103)
+++ phase3/includes/parser/Parser.php	(working copy)
@@ -343,6 +343,7 @@
 		# No more strip!
 		wfRunHooks( 'ParserAfterStrip', array( &$this, &$text, &$this->mStripState ) );
 		$text = $this->internalParse( $text );
+		wfRunHooks( 'ParserAfterParse', array( &$this, &$text, &$this->mStripState ) );
 
 		$text = $this->mStripState->unstripGeneral( $text );
 
Index: extensions/Cite/Cite_body.php
===================================================================
--- extensions/Cite/Cite_body.php	(revision 102780)
+++ extensions/Cite/Cite_body.php	(working copy)
@@ -100,6 +100,14 @@
 	var $mParser;
 
 	/**
+	 * True when the ParserAfterParse hook has been called.
+	 * Used to avoid doing anything in ParserBeforeTidy.
+	 *
+	 * @var boolean
+	 */
+	var $mHaveAfterParse = false;
+
+	/**
 	 * True when a <ref> tag is being processed.
 	 * Used to avoid infinite recursion
 	 *
@@ -1051,11 +1059,17 @@
 	 *
 	 * @return bool
 	 */
-	function checkRefsNoReferences( &$parser, &$text ) {
+	function checkRefsNoReferences( $afterParse, &$parser, &$text ) {
 		if ( $parser->extCite !== $this ) {
-			return $parser->extCite->checkRefsNoReferences( $parser, $text );
+			return $parser->extCite->checkRefsNoReferences( $afterParse, $parser, $text );
 		}
 
+		if ( $afterParse ) {
+			$this->mHaveAfterParse = true;
+		} elseif ( $this->mHaveAfterParse ) {
+			return true;
+		}
+
 		if ( $parser->getOptions()->getIsSectionPreview() ) {
 			return true;
 		}
@@ -1102,7 +1116,8 @@
 
 		if ( !Cite::$hooksInstalled ) {
 			$wgHooks['ParserClearState'][] = array( $parser->extCite, 'clearState' );
-			$wgHooks['ParserBeforeTidy'][] = array( $parser->extCite, 'checkRefsNoReferences' );
+			$wgHooks['ParserAfterParse'][] = array( $parser->extCite, 'checkRefsNoReferences', true );
+			$wgHooks['ParserBeforeTidy'][] = array( $parser->extCite, 'checkRefsNoReferences', false );
 			$wgHooks['InlineEditorPartialAfterParse'][] = array( $parser->extCite, 'checkAnyCalls' );
 			Cite::$hooksInstalled = true;
 		}