Fixes for multi app dir :

Url should be given as relative path (to webroot)
Correct link construction from js

core/js/js.js

@@ -64,9 +64,8 @@ OC={
 			}
 		}else if(file.substring(file.length-3) != 'php' && !isCore){
 			link=OC.appswebroots[app];
-			link+='/'+app+'/';
 			if(type){
-				link+=type+'/';
+				link+= '/'+type+'/';
 			}
 			link+=file;
 		}else{

lib/base.php

@@ -140,9 +140,9 @@ class OC{
 					OC::$APPSROOTS[] = $paths;	
 			}
 		}elseif(file_exists(OC::$SERVERROOT.'/apps')){
-			OC::$APPSROOTS[] = array('path'=> OC::$SERVERROOT.'/apps', 'url' => OC::$WEBROOT.'/apps/', 'writable' => true);
+			OC::$APPSROOTS[] = array('path'=> OC::$SERVERROOT.'/apps', 'url' => '/apps/', 'writable' => true);
 		}elseif(file_exists(OC::$SERVERROOT.'/../apps')){
-			OC::$APPSROOTS[] = array('path'=> rtrim(dirname(OC::$SERVERROOT), '/').'/apps', 'url' => rtrim(dirname(OC::$WEBROOT), '/').'/apps/', 'writable' => true);
+			OC::$APPSROOTS[] = array('path'=> rtrim(dirname(OC::$SERVERROOT), '/').'/apps', 'url' => '/apps/', 'writable' => true);
 			OC::$APPSROOT=rtrim(dirname(OC::$SERVERROOT), '/');
 		}