diff --git a/apps/bookmarks/ajax/addBookmark.php b/apps/bookmarks/ajax/addBookmark.php
index 9241dc8ddf..d66aab5896 100644
--- a/apps/bookmarks/ajax/addBookmark.php
+++ b/apps/bookmarks/ajax/addBookmark.php
@@ -30,6 +30,6 @@ $RUNTIME_NOSETUPFS=true;
 OCP\JSON::checkLoggedIn();
 OCP\JSON::checkAppEnabled('bookmarks');
 
-require_once(OC::$APPSROOT . '/apps/bookmarks/bookmarksHelper.php');
+require_once(OC_App::getAppPath('bookmarks').'/bookmarksHelper.php');
 $id = addBookmark($_GET['url'], $_GET['title'], $_GET['tags']);
 OCP\JSON::success(array('data' => $id));
\ No newline at end of file
diff --git a/apps/calendar/appinfo/remote.php b/apps/calendar/appinfo/remote.php
index 3bd8737ee9..7ab546245f 100644
--- a/apps/calendar/appinfo/remote.php
+++ b/apps/calendar/appinfo/remote.php
@@ -7,8 +7,8 @@
  */
 OCP\App::checkAppEnabled('calendar');
 
-if(substr($_SERVER["REQUEST_URI"],0,strlen(OC::$APPSWEBROOT . '/apps/calendar/caldav.php')) == OC::$APPSWEBROOT . '/apps/calendar/caldav.php'){
-	$baseuri = OC::$APPSWEBROOT . '/apps/calendar/caldav.php';
+if(substr($_SERVER["REQUEST_URI"],0,strlen(OC_App::getAppWebPath('calendar').'/caldav.php')) == OC_App::getAppWebPath('calendar'). '/caldav.php'){
+	$baseuri = OC_App::getAppWebPath('calendar').'/caldav.php';
 }
 
 // only need authentication apps
diff --git a/apps/media/remote.php b/apps/media/remote.php
index 01add42b31..0535077cef 100644
--- a/apps/media/remote.php
+++ b/apps/media/remote.php
@@ -5,7 +5,7 @@ $RUNTIME_APPTYPES=array('filesystem','authentication');
 OC_App::loadApps($RUNTIME_APPTYPES);
 
 if($path_info == '/ampache' || $path_info == '/ampache/'){
-	require_once(OC::$APPSROOT . '/apps/media/index.php');
+	require_once(OC_App::getAppPath('media').'/index.php');
 }else{
-	require_once(OC::$APPSROOT . '/apps/media/server/xml.server.php');
+	require_once(OC_App::getAppPath('media').'/server/xml.server.php');
 }
diff --git a/apps/media/server/xml.server.php b/apps/media/server/xml.server.php
index 6cb6c91ca0..796da130a4 100644
--- a/apps/media/server/xml.server.php
+++ b/apps/media/server/xml.server.php
@@ -22,8 +22,8 @@
 */
 
 OCP\App::checkAppEnabled('media');
- require_once(OC::$APPSROOT . '/apps/media/lib_collection.php');
- require_once(OC::$APPSROOT . '/apps/media/lib_ampache.php');
+ require_once(OC_App::getAppPath('media').'/lib_collection.php');
+ require_once(OC_App::getAppPath('media').'/lib_ampache.php');
 
 $arguments=$_POST;
 if(!isset($_POST['action']) and isset($_GET['action'])){
diff --git a/apps/user_webfinger/webfinger.php b/apps/user_webfinger/webfinger.php
index e75c546c2c..67cbba54a4 100644
--- a/apps/user_webfinger/webfinger.php
+++ b/apps/user_webfinger/webfinger.php
@@ -59,7 +59,7 @@ echo "{\"links\":[";
 $apps = OC_Appconfig::getApps();
 foreach($apps as $app) {
 	if(OCP\App::isEnabled($app)) {
-		if(is_file(OC::$APPSROOT . '/apps/' . $app . '/appinfo/webfinger.php')) {
+		if(is_file(OC_App::getAppPath($app). '/appinfo/webfinger.php')) {
 			require($app . '/appinfo/webfinger.php');
 		}
 	}
diff --git a/lib/app.php b/lib/app.php
index 5883a29bb0..43d60f3a68 100755
--- a/lib/app.php
+++ b/lib/app.php
@@ -571,10 +571,10 @@ class OC_App{
 		//set remote/public handelers
 		$appData=self::getAppInfo($appid);
 		foreach($appData['remote'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'remote_'.$name, '/apps/'.$appid.'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'remote_'.$name, $path);
 		}
 		foreach($appData['public'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'public_'.$name, '/apps/'.$appid.'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'public_'.$name, $appid.'/'.$path);
 		}
 
 		self::setAppTypes($appid);
diff --git a/lib/helper.php b/lib/helper.php
index 550bf9771e..3cf5107eea 100644
--- a/lib/helper.php
+++ b/lib/helper.php
@@ -40,7 +40,7 @@ class OC_Helper {
 		if( $app != '' ){
 			$app .= '/';
 			// Check if the app is in the app folder
-			if( file_exists( OC_App::getAppPath($app).$file )){
+			if( file_exists( OC_App::getAppPath($app).'/'.$file )){
 				if(substr($file, -3) == 'php' || substr($file, -3) == 'css'){	
 					if(substr($app, -1, 1) == '/'){
 						$app = substr($app, 0, strlen($app) - 1);
diff --git a/lib/installer.php b/lib/installer.php
index afe0b9e1bb..bfa34de2a7 100644
--- a/lib/installer.php
+++ b/lib/installer.php
@@ -197,10 +197,10 @@ class OC_Installer{
 
 		//set remote/public handelers
 		foreach($info['remote'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'remote_'.$name, '/apps/'.$info['id'].'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'remote_'.$name, $app.'/'.$path);
 		}
 		foreach($info['public'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'public_'.$name, '/apps/'.$info['id'].'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'public_'.$name, $app.'/'.$path);
 		}
 
 		OC_App::setAppTypes($info['id']);
@@ -287,22 +287,24 @@ class OC_Installer{
 	 * This function installs all apps found in the 'apps' directory that should be enabled by default;
 	 */
 	public static function installShippedApps(){
-		$dir = opendir( OC::$APPSROOT."/apps" );
-		while( false !== ( $filename = readdir( $dir ))){
-			if( substr( $filename, 0, 1 ) != '.' and is_dir(OC::$APPSROOT."/apps/$filename") ){
-				if( file_exists( OC::$APPSROOT."/apps/$filename/appinfo/app.php" )){
-					if(!OC_Installer::isInstalled($filename)){
-						$info=OC_App::getAppInfo($filename);
-						$enabled = isset($info['default_enable']);
-						if( $enabled ){
-							OC_Installer::installShippedApp($filename);
-							OC_Appconfig::setValue($filename,'enabled','yes');
+		foreach(OC::$APPSROOTS as $app_dir) {
+			$dir = opendir( $app_dir['path'] );
+			while( false !== ( $filename = readdir( $dir ))){
+				if( substr( $filename, 0, 1 ) != '.' and is_dir($app_dir['path']."/$filename") ){
+					if( file_exists( $app_dir['path']."/$filename/appinfo/app.php" )){
+						if(!OC_Installer::isInstalled($filename)){
+							$info=OC_App::getAppInfo($filename);
+							$enabled = isset($info['default_enable']);
+							if( $enabled ){
+								OC_Installer::installShippedApp($filename);
+								OC_Appconfig::setValue($filename,'enabled','yes');
+							}
 						}
 					}
 				}
 			}
+			closedir( $dir );
 		}
-		closedir( $dir );
 	}
 
 	/**
@@ -325,10 +327,10 @@ class OC_Installer{
 		
 		//set remote/public handelers
 		foreach($info['remote'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'remote_'.$name, '/apps/'.$app.'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'remote_'.$name, $app.'/'.$path);
 		}
 		foreach($info['public'] as $name=>$path){
-			OCP\CONFIG::setAppValue('core', 'public_'.$name, '/apps/'.$app.'/'.$path);
+			OCP\CONFIG::setAppValue('core', 'public_'.$name, $app.'/'.$path);
 		}
 		
 		OC_App::setAppTypes($info['id']);
diff --git a/public.php b/public.php
index f974e1c50d..19c02a7a02 100644
--- a/public.php
+++ b/public.php
@@ -8,8 +8,8 @@ if(is_null($file)){
 	exit;
 }
 
-$parts=explode('/',$file);
-$app=$parts[2];
+$parts=explode('/',$file,2);
+$app=$parts[0];
 OC_App::loadApp($app);
 
-require_once(OC::$APPSROOT . $file);
+require_once(OC_App::getAppPath($app) .'/'. $parts[1]);
diff --git a/remote.php b/remote.php
index 7131dfc940..55b088d775 100644
--- a/remote.php
+++ b/remote.php
@@ -17,9 +17,9 @@ if(is_null($file)){
 	exit;
 }
 
-$parts=explode('/',$file);
-$app=$parts[2];
+$parts=explode('/', $file, 2);
+$app=$parts[0];
 OC_App::loadApp($app);
 
 $baseuri = OC::$WEBROOT . '/remote.php/'.$service.'/';
-require_once(OC::$APPSROOT . $file);
\ No newline at end of file
+require_once(OC_App::getAppPath($app) .'/'. $parts[1]);
\ No newline at end of file