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I think the OmniFocus Mail Rule works great.

This is quick and probably newbie question:

I assume the Mail Rule for OF doesn't run when is not launched.

Is there any way to run the Mail Rule as a daemon in the background?

As an aside, I'd be interested to hear the long-term vision around the Mail Rule so it becomes more web-resident - something that will naturally happen as we all become more iPhone-enabled :)