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I suggest to add just now simple delete logic to MANY_MANY relation. Not waiting for implementing of link/unlink.
Logic there is straight enough: remove in connection table all records, that related to owner. For example in case of saving article with tags we should just delete from article_tag all records, where article_id = 123. It will be enough for all cases, as later insert command adds all really needed records.
In the meantime we have tests written in AntonTyutin/yii-with-related-behavior@e00fc07 fork.
ps: I have read all related issues and comments