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Steffen, your sense of humor is great, but oftentimes I have no clue what you are talking about. Where does ftruncate factor in?
I was asking what mutt does when it modifies a file in the hopes that it had some pithy algorithm for making sure the mailbox atime and utime conform to the semi-standard you are talking about, so we could steal it.
I'd like to see a solution to this issue. My two problems with your patch are (1) it feels wrong to set the atime earlier than the last actual atime and (2) unconditionally doing the work in flush means it might get set even when there wasn't an intended "new mail" condition.
In other words, I think the fix is ugly :). However, neither of those concerns are necessarily blockers. Practicality beats purity in many cases, and this may be one of them.