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Simply put, this lets you put followup e-mail where it belongs.
Every message has a Message-ID, which is unique, and the registry remembers it. When the message is moved or copied, the registry will notice this and offer the new group as a choice to the splitting strategy.
When a followup is made, usually it mentions the original message's Message-ID in the headers. The registry knows this and uses that mention to find the group where the original message lives. You only have to put a rule like this:
(setq nnimap-my-split-fancy '(|
;; split to parent: you need this
(: gnus-registry-split-fancy-with-parent)
;; other rules, as an example
(: spam-split)
;; default mailbox
"mail")
in your fancy split setup. In addition, you may want to customize the following variables.