I created e.g. a Rlogin menu by some subdirectories under /usr/share/gnome/apps/Rlogin/, 

root@impala:/root(32)# ll /usr/share/gnome/apps/Rlogin/
total 32
...
drwxr-xr-x 2 1000 users 4096 Feb 22 18:54 Homenet/
...
drwxr-xr-x 2 1000 users 4096 May 10  2003 Informatik_pdm/
...
In these subdirectories there are some desktop files:

root@impala:/root(33)# ll /usr/share/gnome/apps/Rlogin/Homenet/
total 144
...
-rw-r--r-- 1 root root 1153 Feb 22 18:54 Beaglebone3_Homenet.desktop
-rw-r--r-- 1 root root  238 Jan 22  2011 Caiman.desktop
...
-rw-r--r-- 1 root root  242 Apr 11  2011 Impala.desktop
...
-rw-r--r-- 1 root root 1103 Apr 19 12:42 Lynx_Homenet.desktop
...



Until gnome-3.6 together with a modified /etc/xdg/menus/applications.menu or a modified /etc/xdg/menus/gnome-applications.menu I got main menu entry Rlogin with submenue entries Homenet, Informatik_pdm etc. In the submenue Homenet I then got then the menu entries for Caiman, Impala, Lynx etc. With gnome-3.8 the submenus Homenet, Informatik_pdm entries disappeared, I then got all entries Caiman, Impala, Lynx etc direct under Rlogin which was already not very convenient. But now with the upgrade to to gnome-3.12 I had only an empty Rlogin entry. It looks, if gnome-3.12 ignores LegacyDir item in /etc/xdg/menus/gnome-applications.menu. After moving the directory Rlogin/ from /usr/share/gnome/apps/ to /usr/share/applications/ my menues appeared again. So only the issue with the missing submenues remains. Is there any way to get application menus with submenus with gnome-3.12.


PS. In /etc/xdg/menus/gnome-applications.menu I had:

  <LegacyDir>/usr/share/gnome/apps</LegacyDir>

  <Menu>
	<Name> Login </Name>
  	<MergeFile>rlogin.menu</MergeFile>
  </Menu>
  ...


And then there is a rlogin.menu file in /etc/xdg/menus/:

<!-- Rlogin -->
<Menu>
   <Name>Rlogin</Name>
       <DirectoryDir>/usr/share/gnom/apps/Rlogin</DirectoryDir>
       <Directory>Rlogin.directory</Directory>

       <Menu>
	  <LegacyDir>/usr/share/gnome/apps/Rlogin/Bioinf_pdm</LegacyDir>
 	  <Name>Bioinf_pdm</Name>
 	  <Directory>.directory</Directory>
	     <Include>
  	        <And>
 	          <Category>Login</Category>
 	    	  <Category>Bioinf_pdm</Category>
      		</And>
	     </Include>
	</Menu>
...
 	<Menu>
 	   <LegacyDir>/usr/share/gnome/apps/Rlogin/Homenet</LegacyDir>
  	   <Name>Homenet</Name>
  	   <Directory>.directory</Directory>
 	     <Include>
   	       <And>
     	     	 <Category>Login</Category>
  	    	 <Category>Homenet</Category>
       	       </And>
 	     </Include>
 	</Menu>
...