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Issue with notifications and Message Carbons. #107
yaxim is using sophisticated logic[tm] to prevent beeping all the time when the phone is on your desk and you chat using the PC. The logic (in the nightly releases as of December 2013) is as follows:
However, all messages, carbons or not, are shown in your chat history (this also includes their XEP-0184 message ack status).
That way, when you are actively chatting on your desktop PC, yaxim will only make one beep and go silent. After you check yaxim for messages, it will beep again, even if your buddy is still messaging your PC client. That way you should neither be bothered by perma-beeping, nor lose wrongly-targeted important messages.
Please let me know if what you are seeing differs from the described behavior, or if it is as described, but is not "the right thing to do". For this, please describe what you would expect, and what happens instead.