When uploading files and selecting files that already exist on the server, the only choices from the File Location drop down is "Root" and "Templates/"

How do we add more locations here? Or get DNN to actually replicate the folder structure under the "Templates/" folder?

1. Create your roles that need to see some things and not others.
2. Go to Host Settings and check that "Auto-Sync File System" is not ticked - it's occasionally buggy and causes files to become invisible
3. Go to Admin, File Manager
4. If you're not seeing some folders you know are there, tick the Recursive box top right and click the Sync icon next to it
5. Create any remaining folders
6. Remove and apply View and/or Write permissions to suit the roles you have  created

Now those roles will only see the desired items on the menus.

Note that there isn't a way to apply permissions to a series of nested folders. Either delete them first, then apply permissions to the top folder and create the folders again inside, or go through and apply permissions to each subfolder one at a time.

That should cover it,
Rob

sorry, I got one thing wrong in my instructions

Leave the Auto-sync File system setting enabled. It was the Scheduled File Sync (DotNetNuke.Services.FileSystem.SynchronizeFileSystem) that causes the problems. It won't be enabled in any case unless you've done so on purpose.

Rob