wounded in the line of duty
It seems like you might be able to accomplish what you want with a bunch of mutt macros around the "limit" and "order" commands.
I'm not sure you'll be able to do everything you want, but it can do a lot.
I don't know of a way to get a view into multiple mailboxes, but otherwise it seems quite possible. Mutt's filtering/selecting is pretty darn fast so it might even work OK to just have everything in a single huge mail folder.
That will be limited because unfortunately mutt doesn't support any truly good mail folder formats (mbox, mmdf, MH, Maildir), but you might use it as an imap client to an imap server that has a good mailbox backend. You could do this with UW IMAP and mix folders; the imap server process doesnt' have to live on a different machine.
If you do this please blog about it more.
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