Index: typo3/sysext/cms/tslib/class.tslib_fe.php
===================================================================
--- typo3/sysext/cms/tslib/class.tslib_fe.php	(revision 6314)
+++ typo3/sysext/cms/tslib/class.tslib_fe.php	(working copy)
@@ -4173,6 +4173,8 @@
 			$this->content = str_replace('"media/', '"'.t3lib_extMgm::siteRelPath('cms').'tslib/media/', $this->content);
 			$this->content = str_replace('"typo3conf/ext/', '"'.$this->absRefPrefix.'typo3conf/ext/', $this->content);
 			$this->content = str_replace('"typo3/contrib/', '"'.$this->absRefPrefix.'typo3/contrib/', $this->content);
+			$this->content = str_replace('"typo3/ext/', '"' . $this->absRefPrefix . 'typo3/ext/', $this->content);
+			$this->content = str_replace('"typo3/sysext/' , '"' . $this->absRefPrefix . 'typo3/sysext/', $this->content);
 			$this->content = str_replace('"'.$GLOBALS['TYPO3_CONF_VARS']['BE']['fileadminDir'], '"'.$this->absRefPrefix.$GLOBALS['TYPO3_CONF_VARS']['BE']['fileadminDir'], $this->content);
 			// Process additional directories
 			$directories = t3lib_div::trimExplode(',', $GLOBALS['TYPO3_CONF_VARS']['FE']['additionalAbsRefPrefixDirectories'], true);
Index: typo3/sysext/cms/tslib/class.tslib_pagegen.php
===================================================================
--- typo3/sysext/cms/tslib/class.tslib_pagegen.php	(revision 6314)
+++ typo3/sysext/cms/tslib/class.tslib_pagegen.php	(working copy)
@@ -671,6 +671,7 @@
 			// JavaScript library files
 		if (is_array($GLOBALS['TSFE']->pSetup['includeJSlibs.'])) {
 			foreach ($GLOBALS['TSFE']->pSetup['includeJSlibs.'] as $key => $JSfile) {
+				if (!is_array($JSfile)) {
 				$ss = $GLOBALS['TSFE']->pSetup['includeJSlibs.'][$key . '.']['external'] ? $JSfile : $GLOBALS['TSFE']->tmpl->getFileName($JSfile);
 				if ($ss) {
 					$type = $GLOBALS['TSFE']->pSetup['includeJSlibs.'][$key . '.']['type'];
@@ -679,19 +680,20 @@
 					}
 					$pageRenderer->addJsLibrary(
 						htmlspecialchars($key),
-						htmlspecialchars($GLOBALS['TSFE']->absRefPrefix . $ss),
+						htmlspecialchars($ss),
 						htmlspecialchars($type),
 						$GLOBALS['TSFE']->pSetup['includeJSlibs.'][$key . '.']['compress'] ? TRUE : FALSE,
 						$GLOBALS['TSFE']->pSetup['includeJSlibs.'][$key . '.']['forceOnTop'] ? TRUE : FALSE,
 						$GLOBALS['TSFE']->pSetup['includeJSlibs.'][$key . '.']['allWrap']
 					);
 				}
-
 			}
 		}
+		}
 
 		if (is_array($GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'])) {
 			foreach ($GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'] as $key => $JSfile) {
+				if (!is_array($JSfile)) {
 				$ss = $GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'][$key . '.']['external'] ? $JSfile : $GLOBALS['TSFE']->tmpl->getFileName($JSfile);
 				if ($ss) {
 					$type = $GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'][$key . '.']['type'];
@@ -700,16 +702,16 @@
 					}
 					$pageRenderer->addJsFooterLibrary(
 						htmlspecialchars($key),
-						htmlspecialchars($GLOBALS['TSFE']->absRefPrefix . $ss),
+						htmlspecialchars($ss),
 						htmlspecialchars($type),
 						$GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'][$key . '.']['compress'] ? TRUE : FALSE,
 						$GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'][$key . '.']['forceOnTop'] ? TRUE : FALSE,
 						$GLOBALS['TSFE']->pSetup['includeJSFooterlibs.'][$key . '.']['allWrap']
 					);
 				}
-
 			}
 		}
+		}
 
 			// JavaScript files
 		if (is_array($GLOBALS['TSFE']->pSetup['includeJS.'])) {
@@ -722,7 +724,7 @@
 							$type = 'text/javascript';
 						}
 						$pageRenderer->addJsFile(
-							htmlspecialchars($GLOBALS['TSFE']->absRefPrefix . $ss),
+							htmlspecialchars($ss),
 							htmlspecialchars($type),
 							$GLOBALS['TSFE']->pSetup['includeJS.'][$key . '.']['compress'] ? TRUE : FALSE,
 							$GLOBALS['TSFE']->pSetup['includeJS.'][$key . '.']['forceOnTop'] ? TRUE : FALSE,
@@ -743,7 +745,7 @@
 							$type = 'text/javascript';
 						}
 						$pageRenderer->addJsFooterFile(
-							htmlspecialchars($GLOBALS['TSFE']->absRefPrefix . $ss),
+							htmlspecialchars($ss),
 							htmlspecialchars($type),
 							$GLOBALS['TSFE']->pSetup['includeFooterJS.'][$key . '.']['compress'] ? TRUE : FALSE,
 							$GLOBALS['TSFE']->pSetup['includeJS.'][$key . '.']['forceOnTop'] ? TRUE : FALSE,