Migrating a project from 3.0 to 3.1 breaks the ability to mark assets as root assets.

[profan]

Release Type: Official Release

Version: 3.1.0.1-beta02-0550

Platform(s): All

Describe the bug
Create a project in 3.0, migrate it to 3.1, try to include any asset as a root asset when under the new 3.1 project structure and find it doesn't get included (like a Scene/GraphicsCompositor).

To Reproduce
Steps to reproduce the behavior:

1. Create a new 3.0 project.
2. Open it in 3.1.0.1-beta02-0550, upgrading it.
3. Create a new Scene or GraphicsCompositor/any asset not included in some property in the editor/serialized that way (and mark it as a root asset).
4. Try to use Content.Load("UrlToAssetHere") and find that the ContentManager does not find the asset, and indeed if you look at the project structure in the actual files, it is not marked as a root asset.

Expected behavior
I expect the upgrade from 3.0 to 3.1 to not break marking things as a root asset.

Additional context
If necessary, I can provide a small repro project..
Also note that this asset has been reported before, but the user closed the issue as they worked around it, but it is still a problem (and I've also personally encountered it now at least twice): #312

[guygodin]

Having the same issue here on a project upgraded from 3.0.0.6 to 3.1