Following the changes to the project structure and the appxmanifest schema, I decided to put together a small Visual Studio 2015 extension to upgrade the existing Windows Store 8.1 and Windows Phone 8.1 (not Silverlight) projects to Windows 10 UAP applications.
After the extension is installed, you will have an additional menu item in the project file context menu.
The retargeting process adjusts the project file and make changes to the Package.appxmanifest file.
NOTE: The retarget menu item will only be available on Windows Store 8.1 (C#) and Windows Phone 8.1 (C#) projects.
Keep in mind you still might need to change couple of things in the project to get it running. (e.g. Phone specific styles left from Windows Phone 8.1 implementation, Tile sizes left from the Windows Store application - in the new package manifest the tile sizes are the same as the phone package manifest from 8.1)