Index: tests/phpunit/includes/GlobalFunctions/GlobalTest.php
===================================================================
--- tests/phpunit/includes/GlobalFunctions/GlobalTest.php	(revision 101480)
+++ tests/phpunit/includes/GlobalFunctions/GlobalTest.php	(working copy)
@@ -831,42 +831,42 @@
 	}
 
 	/**
-	 * @dataProvider provideMakeUrlIndex()
+	 * @dataProvider provideMakeUrlIndexes()
 	 */
-	function testMakeUrlIndex( $url, $expected ) {
-		$index = wfMakeUrlIndex( $url );
-		$this->assertEquals( $expected, $index, "wfMakeUrlIndex(\"$url\")" );
+	function testMakeUrlIndexes( $url, $expected ) {
+		$index = wfMakeUrlIndexes( $url );
+		$this->assertEquals( $expected, $index, "wfMakeUrlIndexes(\"$url\")" );
 	}
 
-	function provideMakeUrlIndex() {
+	function provideMakeUrlIndexes() {
 		return array(
 			array(
 				// just a regular :)
 				'https://bugzilla.wikimedia.org/show_bug.cgi?id=28627',
-				'https://org.wikimedia.bugzilla./show_bug.cgi?id=28627'
+				array( 'https://org.wikimedia.bugzilla./show_bug.cgi?id=28627' )
 			),
 			array(
 				// mailtos are handled special
 				// is this really right though? that final . probably belongs earlier?
 				'mailto:wiki@wikimedia.org',
-				'mailto:org.wikimedia@wiki.',
+				array( 'mailto:org.wikimedia@wiki.' )
 			),
 
 			// file URL cases per bug 28627...
 			array(
 				// three slashes: local filesystem path Unix-style
 				'file:///whatever/you/like.txt',
-				'file://./whatever/you/like.txt'
+				array( 'file://./whatever/you/like.txt' )
 			),
 			array(
 				// three slashes: local filesystem path Windows-style
 				'file:///c:/whatever/you/like.txt',
-				'file://./c:/whatever/you/like.txt'
+				array( 'file://./c:/whatever/you/like.txt' )
 			),
 			array(
 				// two slashes: UNC filesystem path Windows-style
 				'file://intranet/whatever/you/like.txt',
-				'file://intranet./whatever/you/like.txt'
+				array( 'file://intranet./whatever/you/like.txt' )
 			),
 			// Multiple-slash cases that can sorta work on Mozilla
 			// if you hack it just right are kinda pathological,
@@ -875,6 +875,15 @@
 			//
 			// Those will survive the algorithm but with results that
 			// are less consistent.
+
+			// protocol-relative URL cases per bug 29854...
+			array(
+				'//bugzilla.wikimedia.org/show_bug.cgi?id=28627',
+				array(
+					'http://org.wikimedia.bugzilla./show_bug.cgi?id=28627',
+					'https://org.wikimedia.bugzilla./show_bug.cgi?id=28627'
+				)
+			),
 		);
 	}
 	
Index: includes/GlobalFunctions.php
===================================================================
--- includes/GlobalFunctions.php	(revision 101480)
+++ includes/GlobalFunctions.php	(working copy)
@@ -605,12 +605,12 @@
 }
 
 /**
- * Make a URL index, appropriate for the el_index field of externallinks.
+ * Make URL indexes, appropriate for the el_index field of externallinks.
  *
  * @param $url String
- * @return String
+ * @return array
  */
-function wfMakeUrlIndex( $url ) {
+function wfMakeUrlIndexes( $url ) {
 	$bits = wfParseUrl( $url );
 
 	// Reverse the labels in the hostname, convert to lower case
@@ -650,7 +650,12 @@
 	if ( isset( $bits['fragment'] ) ) {
 		$index .= '#' . $bits['fragment'];
 	}
-	return $index;
+
+	if ( $prot == '' ) {
+		return array( "http:$index", "https:$index" );
+	} else {
+		return array( $index );
+	}
 }
 
 /**
Index: includes/installer/MysqlUpdater.php
===================================================================
--- includes/installer/MysqlUpdater.php	(revision 101480)
+++ includes/installer/MysqlUpdater.php	(working copy)
@@ -189,7 +189,8 @@
 			array( 'doMigrateUserOptions' ),
 			array( 'dropField', 'user',         'user_options', 'patch-drop-user_options.sql' ),
 			array( 'addField', 'revision',      'rev_sha1',         'patch-rev_sha1.sql' ),
-			array( 'addField', 'archive',       'ar_sha1',          'patch-ar_sha1.sql' )
+			array( 'addField', 'archive',       'ar_sha1',          'patch-ar_sha1.sql' ),
+			array( 'doExtLinksProtocolRelativeUpdate' ),
 		);
 	}
 
@@ -850,4 +851,56 @@
 		$this->applyPatch( 'patch-user-newtalk-timestamp-null.sql' );
 		$this->output( "done.\n" );
 	}
+
+	protected function doExtLinksProtocolRelativeUpdate() {
+		$this->output( "Updating externallinks table to fix indexes for protocol-relative URLs...\n" );
+		if ( wfGetLB()->getServerCount() > 1 ) {
+			// Slow, replication-friendly update
+			$res = $this->db->select( 'externallinks', array( 'el_from', 'el_to', 'el_index' ),
+				array( 'el_index' . $this->db->buildLike( '//', $this->db->anyString() ) ), __METHOD__ );
+			$count = 0;
+			foreach ( $res as $row ) {
+				$count = ( $count + 1 ) % 100;
+				if ( $count == 0 ) {
+					wfWaitForSlaves();
+				}
+				$this->db->insert( 'externallinks',
+					array(
+						'el_from' => $row->el_from,
+						'el_to' => $row->el_to,
+						'el_index' => "http:$row->el_index",
+					), __METHOD__
+				);
+				$this->db->update( 'externallinks',
+					array(
+						'el_index' => "https:$row->el_index",
+					),
+					array(
+						'el_from' => $row->el_from,
+						'el_to' => $row->el_to,
+						'el_index' => $row->el_index,
+					), __METHOD__
+				);
+			}
+		} else {
+			// Fast update
+			$this->db->insertSelect( 'externallinks', 'externallinks',
+				array(
+					'el_from' => 'el_from',
+					'el_to' => 'el_to',
+					'el_index' => 'CONCAT(\'http:\', el_index)'
+				), array(
+					'el_index ' . $this->db->buildLike( '//', $this->db->anyString() )
+				), __METHOD__
+			);
+			$this->db->update( 'externallinks',
+				array(
+					'el_index = CONCAT(\'https:\', el_index)'
+				), array(
+					'el_index ' . $this->db->buildLike( '//', $this->db->anyString() )
+				), __METHOD__
+			);
+		}
+		$this->output( "Done.\n" );
+	}
 }
Index: includes/LinksUpdate.php
===================================================================
--- includes/LinksUpdate.php	(revision 101480)
+++ includes/LinksUpdate.php	(working copy)
@@ -456,11 +456,13 @@
 		$arr = array();
 		$diffs = array_diff_key( $this->mExternals, $existing );
 		foreach( $diffs as $url => $dummy ) {
-			$arr[] = array(
-				'el_from'   => $this->mId,
-				'el_to'     => $url,
-				'el_index'  => wfMakeUrlIndex( $url ),
-			);
+			foreach( wfMakeUrlIndexes( $url ) as $index ) {
+				$arr[] = array(
+					'el_from'   => $this->mId,
+					'el_to'     => $url,
+					'el_index'  => $index,
+				);
+			}
 		}
 		return $arr;
 	}
Index: includes/api/ApiQueryExternalLinks.php
===================================================================
--- includes/api/ApiQueryExternalLinks.php	(revision 101480)
+++ includes/api/ApiQueryExternalLinks.php	(working copy)
@@ -69,6 +69,11 @@
 			$this->addOption( 'ORDER BY', 'el_from' );
 		}
 
+		// If we're querying all protocols, use DISTINCT to avoid repeating protocol-relative links twice
+		if ( $protocol === null ) {
+			$this->addOption( 'DISTINCT' );
+		}
+
 		$this->addOption( 'LIMIT', $params['limit'] + 1 );
 		$offset = isset( $params['offset'] ) ? $params['offset'] : 0;
 		if ( $offset ) {