Per Ken Rosenthal, he just signed a long-term extension with the club, which will be effective regardless of if he becomes permanent GM or not. I think he had a good chance of getting the job before (it's pretty much an identical role to his previous one as Assistant GM, given how baseball front offices are restructuring) but this makes me think he has an even better chance now.
And, to clarify what's going on in Toronto a little bit, they're one of the clubs going with the "title inflation" strategy for their front office personnel, which can act as a way to accumulate more front office talent. Basically, the President is the new GM, the GM is the new Assistant GM, and the titles under that are more or less arbitrary (and sometimes misleading, so that other teams can't easily identify members to poach).
Anthopolous was regarded as a dead man walking heading into this year if the Jays didn't make the playoffs. They tried to hire Duquette from Baltimore last offseason, then despite being in good position to make the playoffs they went out and hired Mark Shapiro away from the Indians during this season to be their new President of Baseball Ops. They made, IMO, a courtesy offer to Anthopolous, who obviously walked away from it because he was taking a clear step back in terms of role and responsibility. He had also more or less gutted their farm system, was told by Shapiro that he thought he'd pushed too many chips in, and likely knew if/when the Jays fall off that he'd be the first one blamed/fired.
Basically, it all comes back to the President being the new GM in baseball's current front office structure.
