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As long as we're talking about sorting flagged items, and context mode views in general, here's an implementation consideration.

How do you define the behavior when sorting only a subset of the list? Suppose I have the following flagged items:

Task 1@Context 1
Task 2@Context 2
Task 3@Context 1
Task 4@Context 2
Task 5@Context 2
Task 6@Context 1
Task 7@Context 3
Task 8@Context 3

I decide that Task 8 is the most important task, so I move it to the top of the list. Fine. Result looks like this:

Task 8@Context 3
Task 1@Context 1
Task 2@Context 2
Task 3@Context 1
Task 4@Context 2
Task 5@Context 2
Task 6@Context 1
Task 7@Context 3

Now what if I had been looking at a subset of the list when I did that? Suppose I was looking only at Context 3:

Task 7@Context 3
Task 8@Context 3

I move Task 8 to the top of that list. If I go back to the full view, is Task 8 at the top of the list, or somewhere in the middle?

Okay, I hear you say that the only reasonable place to put Task 8 is just before Task 7, regardless of where they are in the list. That makes for asymmetrical behavior, in that the first context will be special in a way that others are not, where moving an action to the top of its list will move it to the top of the overall list, but it isn't too hard to document that. We'll press on.

Suppose we were just looking at Context 2:
Task 2@Context 2
Task 4@Context 2
Task 5@Context 2

I move Task 5 above Task 4, so the new list is:
Task 2@Context 2
Task 5@Context 2
Task 4@Context 2

Now I go back to the full list. Is it

Task 1@Context 1
Task 2@Context 2
Task 3@Context 1
Task 5@Context 2
Task 4@Context 2
Task 6@Context 1
Task 7@Context 3
Task 8@Context 3

or is it

Task 1@Context 1
Task 2@Context 2
Task 5@Context 2
Task 3@Context 1
Task 4@Context 2
Task 6@Context 1
Task 7@Context 3
Task 8@Context 3

What if we flag additional items or create additional flagged items, where do they go?

This is all straightforward compared to sorting of contexts. I select context A, and shuffle its actions into my desired order. Now I select context B and do the same. When I select both A & B for viewing, what is the result? Do I put the first context's info up first (first context being the one that appears closest to the top of the sidebar), followed by the second context's? What happens when I then rearrange the combined view so that the two are mingled? What happens when I rearrange the order of the contexts? If I select a third context which hasn't had any manual sorting, where are its actions placed in the view, and what ordering do they have?

Sounds like a delightful feature to implement, document, test and comprehend. In the end, the users generally won't be any better off, because it will be one more thing to fiddle with endlessly instead of draining the swamp, and the Omni development staff will have spent countless precious hours of their limited time implementing this instead of something that might bring substantial results.