On the face of it, this wouldn’t appear to be the way PayPal (s ebay) wanted to start off its year. The company is poised to begin rolling out a big initiative to bring its payment system into physical retail stores, part of an ambitious effort to open up PayPal’s business beyond online and simple mobile payments. Now it has to move forward without its president, Scott Thompson, who is leaving to become the CEO of Yahoo(s yhoo).

But more than the story about Thompson leaving, his departure signals the changing face of eBay, which increasingly looks at PayPal as its crown jewel. And who better to safeguard that than the man at the top? EBay CEO John Donohoe has announced he will take over PayPal as interim president for the time being. But from a source, we hear that Donohoe may be looking at keeping the title for…

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