diff --git a/htdocs/admin/menus.php b/htdocs/admin/menus.php
index 757eb250ca2..914d4e66abb 100644
--- a/htdocs/admin/menus.php
+++ b/htdocs/admin/menus.php
@@ -39,12 +39,13 @@ $langs->load("other");
 // Security check
 if (!$user->admin) accessforbidden();
 
-$dirstandard = array("/core/menus/standard");
-$dirsmartphone = array("/core/menus/smartphone");
-foreach($conf->menus_modules as $dir)
+$dirstandard = array();
+$dirsmartphone = array();
+$dirmenus=array_merge(array("/core/menus/"),(array) $conf->modules_parts['menus']);
+foreach($dirmenus as $dirmenu)
 {
-    $dirstandard[]=$dir.'standard';
-    $dirsmartphone[]=$dir.'standard';
+    $dirstandard[]=$dirmenu.'standard';
+    $dirsmartphone[]=$dirmenu.'smartphone';
 }
 
 
diff --git a/htdocs/admin/menus/index.php b/htdocs/admin/menus/index.php
index a05567af734..b99893d553b 100644
--- a/htdocs/admin/menus/index.php
+++ b/htdocs/admin/menus/index.php
@@ -32,12 +32,13 @@ $langs->load("admin");
 
 if (! $user->admin) accessforbidden();
 
-$dirstandard = array("/core/menus/standard");
-$dirsmartphone = array("/core/menus/smartphone");
-foreach($conf->menus_modules as $dir)
+$dirstandard = array();
+$dirsmartphone = array();
+$dirmenus=array_merge(array("/core/menus/"),(array) $conf->modules_parts['menus']);
+foreach($dirmenus as $dirmenu)
 {
-    $dirstandard[]=$dir.'standard';
-    $dirsmartphone[]=$dir.'standard';
+    $dirstandard[]=$dirmenus.'standard';
+    $dirsmartphone[]=$dirmenus.'smartphone';
 }
 
 $mesg=$_GET["mesg"];
diff --git a/htdocs/admin/system/constall.php b/htdocs/admin/system/constall.php
index 243b3846232..a7c27179818 100644
--- a/htdocs/admin/system/constall.php
+++ b/htdocs/admin/system/constall.php
@@ -178,6 +178,7 @@ foreach($configfileparameters as $key)
 			else if ($newkey == 'dolibarr_main_url_root' && preg_match('/__auto__/',${$newkey})) print ${$newkey}.' => '.constant('DOL_MAIN_URL_ROOT');
 			else if ($newkey == 'dolibarr_main_url_root_alt' && preg_match('/__auto__/',${$newkey})) print ${$newkey}.' => '.constant('DOL_MAIN_URL_ROOT_ALT');
 			else print ${$newkey};
+			if ($newkey == 'dolibarr_main_url_root' && $newkey != DOL_MAIN_URL_ROOT) print ' (currently used by autodetect: '.DOL_MAIN_URL_ROOT.')';
 			print "</td>";
 		}
 		print "</tr>\n";
@@ -242,7 +243,8 @@ if ($resql)
 
 print '</table>';
 
-$db->close();
 
 llxFooter();
+
+$db->close();
 ?>
diff --git a/htdocs/cashdesk/class/Auth.class.php b/htdocs/cashdesk/class/Auth.class.php
index a6868aa1814..7eec78ebd32 100644
--- a/htdocs/cashdesk/class/Auth.class.php
+++ b/htdocs/cashdesk/class/Auth.class.php
@@ -102,7 +102,7 @@ class Auth
         $authmode=explode(',',$dolibarr_main_authentication);
 
         // No authentication mode
-        if (! count($authmode) && empty($conf->login_modules))
+        if (! count($authmode))
         {
             $langs->load('main');
             dol_print_error('',$langs->trans("ErrorConfigParameterNotDefined",'dolibarr_main_authentication'));
diff --git a/htdocs/core/class/conf.class.php b/htdocs/core/class/conf.class.php
index 5f8185253ed..2914a1aecd1 100644
--- a/htdocs/core/class/conf.class.php
+++ b/htdocs/core/class/conf.class.php
@@ -52,17 +52,12 @@ class Conf
 	public $smart_menu;
 
 	public $modules					= array();	// List of activated modules
-	public $modules_parts			= array('triggers'=>array(),'login'=>array(),'substitutions'=>array(),'menus'=>array(),'theme'=>array(),'tpl'=>array(),'barcode'=>array(),'models'=>array());	// List of modules parts
+	public $modules_parts			= array('js'=>array(),'triggers'=>array(),'login'=>array(),'substitutions'=>array(),'menus'=>array(),'theme'=>array(),'tpl'=>array(),'barcode'=>array(),'models'=>array());	// List of modules parts
 
-	// TODO Remove all thoose tabs with one generic
-	public $triggers_modules		= array();
-	public $login_modules			= array();
-	public $substitutions_modules	= array();
-	public $menus_modules			= array();
-	public $barcode_modules			= array();
-	public $sms_engine_modules		= array();
-	public $css_modules				= array();
+	// TODO Remove thoose arrays with generic module_parts
 	public $tabs_modules			= array();
+	public $sms_engine_modules		= array();
+	// TODO Remove thoose arrays with generic module_parts
 	public $hooks_modules			= array();
 	public $societe_modules	        = array();
 
@@ -183,15 +178,15 @@ class Conf
 						{
 							$modulename = strtolower($reg[1]);
 							$partname = strtolower($reg[2]);
-							$varname = $partname.'_modules';  // TODO deprecated
-							if (! isset($this->$varname) || ! is_array($this->$varname)) { $this->$varname = array(); } // TODO deprecated
+							//$varname = $partname.'_modules';  // TODO deprecated
+							//if (! isset($this->$varname) || ! is_array($this->$varname)) { $this->$varname = array(); } // TODO deprecated
 							if (! isset($this->modules_parts[$partname]) || ! is_array($this->modules_parts[$partname])) { $this->modules_parts[$partname] = array(); }
 							$arrValue = json_decode($value,true);
 							if (is_array($arrValue) && ! empty($arrValue)) $value = $arrValue;
 							else if (in_array($partname,array('login','menus','substitutions','triggers','tpl','theme'))) $value = '/'.$modulename.'/core/'.$partname.'/';
 							else if (in_array($partname,array('models'))) $value = '/'.$modulename.'/';
 							else if ($value == 1) $value = '/'.$modulename.'/core/modules/'.$partname.'/';
-							$this->$varname = array_merge($this->$varname, array($modulename => $value));  // TODO deprecated
+							//$this->$varname = array_merge($this->$varname, array($modulename => $value));  // TODO deprecated
 							$this->modules_parts[$partname] = array_merge($this->modules_parts[$partname], array($modulename => $value));
 						}
                         // If this is a module constant (must be at end)
diff --git a/htdocs/core/lib/functions.lib.php b/htdocs/core/lib/functions.lib.php
index eeff6e48068..bac8f90d211 100644
--- a/htdocs/core/lib/functions.lib.php
+++ b/htdocs/core/lib/functions.lib.php
@@ -3370,7 +3370,7 @@ function complete_substitutions_array(&$substitutionarray,$outputlangs,$object='
     require_once(DOL_DOCUMENT_ROOT.'/core/lib/files.lib.php');
 
     // Check if there is external substitution to do asked by plugins
-    $dirsubstitutions=array_merge(array(),$conf->modules_parts['substitutions']);
+    $dirsubstitutions=array_merge(array(),(array) $conf->modules_parts['substitutions']);
 
     foreach($dirsubstitutions as $reldir)
     {
diff --git a/htdocs/core/lib/security2.lib.php b/htdocs/core/lib/security2.lib.php
index aa5209af653..bd8ef60f3e1 100644
--- a/htdocs/core/lib/security2.lib.php
+++ b/htdocs/core/lib/security2.lib.php
@@ -61,51 +61,49 @@ function checkLoginPassEntity($usertotest,$passwordtotest,$entitytotest,$authmod
 	$login = '';
 
 	// Validation of login/pass/entity with a third party login module method
-	if (! empty($conf->login_modules) && is_array($conf->login_modules))
-	{
-    	foreach($conf->login_modules as $reldir)
-    	{
-    	    $dir=dol_buildpath($reldir,0);
+	$dirlogin=array_merge(array("/core/login"),(array) $conf->modules_parts['login']);
+	foreach($dirlogin as $reldir)
+   	{
+   	    $dir=dol_buildpath($reldir,0);
 
-    	    $newdir=dol_osencode($dir);
+   	    $newdir=dol_osencode($dir);
 
-    		// Check if directory exists
-    		if (! is_dir($newdir)) continue;
+   		// Check if directory exists
+   		if (! is_dir($newdir)) continue;
 
-    		$handle=opendir($newdir);
-    		if (is_resource($handle))
-    		{
-    			while (($file = readdir($handle))!==false)
-    			{
-    				if (is_readable($dir.'/'.$file) && preg_match('/^functions_([^_]+)\.php/',$file,$reg))
-    				{
-    					$authfile = $dir.'/'.$file;
-    					$mode = $reg[1];
+   		$handle=opendir($newdir);
+   		if (is_resource($handle))
+   		{
+   			while (($file = readdir($handle))!==false)
+   			{
+   				if (is_readable($dir.'/'.$file) && preg_match('/^functions_([^_]+)\.php/',$file,$reg))
+   				{
+   					$authfile = $dir.'/'.$file;
+   					$mode = $reg[1];
 
-    					$result=include_once($authfile);
-    					if ($result)
-    					{
-    						// Call function to check user/password
-    						$function='check_user_password_'.$mode;
-    						$login=call_user_func($function,$usertotest,$passwordtotest,$entitytotest);
-    						if ($login)
-    						{
-            					$conf->authmode=$mode;	// This properties is defined only when logged to say what mode was successfully used
-    						}
-    					}
-    					else
-    					{
-    						dol_syslog("Authentification ko - failed to load file '".$authfile."'",LOG_ERR);
-    						sleep(1);    // To slow brut force cracking
-    						$langs->load('main');
-    						$langs->load('other');
-    						$_SESSION["dol_loginmesg"]=$langs->trans("ErrorFailedToLoadLoginFileForMode",$mode);
-    					}
-    				}
-    			}
-    		    closedir($handle);
-    		}
-    	}
+   					$result=include_once($authfile);
+   					if ($result)
+   					{
+   						// Call function to check user/password
+   						$function='check_user_password_'.$mode;
+   						$login=call_user_func($function,$usertotest,$passwordtotest,$entitytotest);
+   						if ($login)
+   						{
+           					$conf->authmode=$mode;	// This properties is defined only when logged to say what mode was successfully used
+   						}
+   					}
+   					else
+   					{
+   						dol_syslog("Authentification ko - failed to load file '".$authfile."'",LOG_ERR);
+   						sleep(1);    // To slow brut force cracking
+   						$langs->load('main');
+   						$langs->load('other');
+   						$_SESSION["dol_loginmesg"]=$langs->trans("ErrorFailedToLoadLoginFileForMode",$mode);
+   					}
+   				}
+   			}
+   		    closedir($handle);
+  		}
 	}
 
 	// Validation of login/pass/entity with standard modules
diff --git a/htdocs/filefunc.inc.php b/htdocs/filefunc.inc.php
index 30b23141e62..1a15ed81d99 100755
--- a/htdocs/filefunc.inc.php
+++ b/htdocs/filefunc.inc.php
@@ -78,7 +78,6 @@ if (! $result && ! empty($_SERVER["GATEWAY_INTERFACE"]))    // If install not do
 	header("Location: install/index.php");
 	exit;
 }
-
 // Disable php display errors
 if (! empty($dolibarr_main_prod)) ini_set('display_errors','Off');
 
@@ -149,7 +148,7 @@ $concatpath='';
 foreach($paths as $tmppath)
 {
     if ($tmppath) $concatpath.='/'.$tmppath;
-    //print $real_$dolibarr_main_document_root.'-'.realpath($pathroot.$concatpath).'<br>';
+    //print $_SERVER["SCRIPT_NAME"].'-'.$pathroot.'-'.$concatpath.'-'.$real_dolibarr_main_document_root.'-'.realpath($pathroot.$concatpath).'<br>';
     if ($real_dolibarr_main_document_root == @realpath($pathroot.$concatpath))    // @ avoid warning when safe_mode is on.
     {
         $tmp3=$concatpath;
@@ -157,7 +156,9 @@ foreach($paths as $tmppath)
         $found=1;
         break;
     }
+    //else print "Not found yet for concatpath=".$concatpath."<br>\n";
 }
+
 if (! $found)	// If autodetect fails (Ie: when using apache alias that point outside default DOCUMENT_ROOT.
 {
 	$tmp=$dolibarr_main_url_root;
diff --git a/htdocs/main.inc.php b/htdocs/main.inc.php
index 4076699e201..0678797c8aa 100644
--- a/htdocs/main.inc.php
+++ b/htdocs/main.inc.php
@@ -310,7 +310,7 @@ if (! defined('NOLOGIN'))
     $authmode=explode(',',$dolibarr_main_authentication);
 
     // No authentication mode
-    if (! count($authmode) && empty($conf->login_modules))
+    if (! count($authmode))
     {
         $langs->load('main');
         dol_print_error('',$langs->trans("ErrorConfigParameterNotDefined",'dolibarr_main_authentication'));
@@ -893,16 +893,14 @@ function top_htmlhead($head, $title='', $disablejs=0, $disablehead=0, $arrayofjs
         //print 'themepath='.$themepath.' themeparam='.$themeparam;exit;
         print '<link rel="stylesheet" type="text/css" title="default" href="'.$themepath.$themeparam.'">'."\n";
         // CSS forced by modules (relative url starting with /)
-        if (is_array($conf->css_modules))
+        $dircss=(array) $conf->modules_parts['css'];
+        foreach($dircss as $key => $cssfile)
         {
-            foreach($conf->css_modules as $key => $cssfile)
-            {
-                // cssfile is an absolute path
-                print '<link rel="stylesheet" type="text/css" title="default" href="'.dol_buildpath($cssfile,1);
-                // We add params only if page is not static, because some web server setup does not return content type text/css if url has parameters, so browser cache is not used.
-                if (!preg_match('/\.css$/i',$cssfile)) print $themeparam;
-                print '"><!-- Added by module '.$key. '-->'."\n";
-            }
+            // cssfile is a relative path
+            print '<link rel="stylesheet" type="text/css" title="default" href="'.dol_buildpath($cssfile,1);
+            // We add params only if page is not static, because some web server setup does not return content type text/css if url has parameters, so browser cache is not used.
+            if (!preg_match('/\.css$/i',$cssfile)) print $themeparam;
+            print '"><!-- Added by module '.$key. '-->'."\n";
         }
         // CSS forced by page in top_htmlhead call (relative url starting with /)
         if (is_array($arrayofcss))
@@ -1033,7 +1031,14 @@ function top_htmlhead($head, $title='', $disablejs=0, $disablehead=0, $arrayofjs
             // Add datepicker default options
             print '<script type="text/javascript" src="'.DOL_URL_ROOT.'/core/js/datepicker.js.php?lang='.$langs->defaultlang.'"></script>'."\n";
 
-            // Output module javascript
+            // JS forced by modules (relative url starting with /)
+            $dirjs=(array) $conf->modules_parts['js'];
+            foreach($dirjs as $key => $jsfile)
+            {
+            	// jsfile is a relative path
+            	print '<script type="text/javascript" src="'.dol_buildpath($jsfile,1).'"></script><!-- Added by module '.$key. '-->'."\n";
+            }            
+            // JS forced by page in top_htmlhead (relative url starting with /)
             if (is_array($arrayofjs))
             {
                 print '<!-- Includes JS specific to page -->'."\n";
@@ -1189,7 +1194,7 @@ function top_menu($head, $title='', $target='', $disablejs=0, $disablehead=0, $a
     if (! class_exists('MenuTop'))
     {
         $menufound=0;
-        $dirmenus=array_merge(array("/core/menus/"),$conf->modules_parts['menus']);
+        $dirmenus=array_merge(array("/core/menus/"),(array) $conf->modules_parts['menus']);
         foreach($dirmenus as $dirmenu)
         {
             $menufound=dol_include_once($dirmenu."standard/".$top_menu);
@@ -1395,7 +1400,7 @@ function left_menu($menu_array_before, $helppagename='', $moresearchform='', $me
     if (! class_exists('MenuLeft'))
     {
         $menufound=0;
-        $dirmenus=array_merge(array("/core/menus/"),$conf->modules_parts['menus']);
+        $dirmenus=array_merge(array("/core/menus/"),(array) $conf->modules_parts['menus']);
         foreach($dirmenus as $dirmenu)
         {
             $menufound=dol_include_once($dirmenu."standard/".$left_menu);