So maybe you read my last post on MDT Application Organization that had to do with MDT Applications Without Source Files. Well this does have some Linked Deployment Share issues that I have detailed, but there is an alternate method to MDT Application Organization when you want to use MDT Application Source Files.
For starters, head over to Notepad++ and download and install the latest version. Once you install and open Notepad++, from the Menu, select Plugins and then Plugin Manager and Show Plugin Manager. Check XML Tools (I also recommend adding Compare) and press Install. You will need to restart Notepad++
Now that you have XML Tools installed, make sure MDT is closed and open Control\Applications.xml from your Deployment Share. Now select from the Menu, Plugins, XML Tools, Pretty print (XML only – with line breaks). This will make the Applications.xml change from a single line to a properly formatted XML file.
Now modify the Application you want by editing the path in the Source and WorkingDirectory tags.
Save the XML and move your content in the Applications directory of your Deployment Share. Now you can organize your Applications and still have Linked Deployment Shares.