I'm in an awkward spot and want some outside perspective.
I'm an international Master's student wrapping up soon. I've been talking with a potential PhD supervisor in a different department at the same university. We've discussed the research and the project, he's confirmed funding, introduced me to his group, and told me to go ahead and apply. Research fit and supervisory style both feel right.
The complication is references. My current supervisor has said more than once that he'd like me to stay on for a PhD with him. The relationship is fine on the surface, but I don't think it would land well if he knew I was applying elsewhere. Based on how he's handled a similar situation before, I'd expect things to get unpleasant. There have also been some interpersonal issues in the lab that I'd rather not stick around for, which is why I want to move on. My gut tells me that if I even give him a hint that I'm applying somewhere, he will sabotage my MSc defence (at least that is what I heard from previous students )
So my question: how bad does it look if all three of my references are from my undergrad rather than my current Master's supervisor? Is the absence of a current-supervisor reference something admissions committees actually flag, or is it more common than I think? The program also explicitly asks for at least 1 professional ref