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2) Would flags work for you?
Yes, it would be a start, but I would see the need to have at least two variations— one for projects that were on fire and urgent. The other for projects that were active, but dead for various reasons-- the need to refactor, the lack of next actions, etc.

3) I'm not sure I understand what you mean.

Attached is sub-projects being displayed in the project window. As you probably know, in OmniOutliner, when you double click on an item in the utility drawer, you see the items underneath it. These would be equivalent to subprojects.
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