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The issue:

Say a new message arrives in my inbox that is a reply to an existing thread/chain of emails that I've archived. mu4e will move the entire thread out of the archive and back into my inbox.

The question:

Is there a way to stop mu4e from moving the whole thread out of archive and back into my inbox? For context, in Gmail this can be accomplished by turning "conversation grouping" off.

I am a mu4e newb, but digging it so far. Any help with the issue I'm encountering would be much appreciated.

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You may have display of "related messages" turned on. Try pressing W (note: capital) while in your inbox (mu4e-headers-toggle-include-related) and seeing if those messages disappear.

If this is what is happening then those messages you were seeing weren't being "moved" back from where they were archived to; mu4e is including them in the inbox headers list for your convenience. It will also show your replies to inbox messages (which will be in some "sent" folder), or messages in the thread that you'd manually moved to any other folder.

Related messages is described in the mu4e documentation: https://www.djcbsoftware.nl/code/mu/mu4e/Other-search-functionality.html#Including-related-messages

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