Cherrifaery, I just wanted to say your initial post is about the calmest I could have possibly imagined in that situation. Major kudos for no references to power tools, waterboarding, or strangulation. I think snowcapk's advice is very good, about trying to find someone in your department who can mediate between you and your advisor. I suppose I would try to make progress on the overall dynamic between yourself and your advisor (with outside help if possible) before enquiring about that particular comment on the rec. I don't really have anything else to add other than to say some anonymous dude on the internet sympathizes with you and admires your composure.
