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Chip Kelly: Colin Kaepernick staying with 49ers ‘never been a question’

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San Francisco 49ers head coach Chip Kelly became the second member of the organization’s power structure to unequivocally state in recent days that there is no doubt that Colin Kaepernick will be with the team after April 1, when $12 million of his $14 million salary for 2016 becomes fully guaranteed.

In fact, the first-year Niners coach is at a loss over why it’s become such a huge topic of conversation.

“I don’t know what the narrative is, that ‘Is he on the team? Is he not on the team?’ That’s never been a question,” Kelly told reporters at the NFL Scouting Combine Thursday, via the San Jose Mercury News. “I’m excited about working with Colin.”

Kelly’s comments echo what 49ers general manager Troy Baalke said on Wednesday when stating he “absolutely” expects Kaepernick to remain with the team.

Before Kelly’s arrival, it was widely believed that Kaepernick’s career with the 49ers organization had reached a point of no return and that one way or another the two parties would go their separate ways. There appeared to be a level of mistrust between the quarterback and the team, illustrated by how Kaepernick recently underwent three surgeries — to his left shoulder, left knee and right thumb — in Vail, Colo., and not by team doctors at Stanford Hospital.

But Kaepernick’s unique skill set — not to mention the fact that he has proven he can be an excellent quarterback — seemed to mesh well with Kelly’s mad scientist-inspired offensive system.

Kelly also indicated that there’s nothing he has seen or heard in his dealings with the 28-year-old signal-caller that indicates he’s unhappy with the the situation as it stands.

“He wants to be here. He’s never expressed to me that he didn’t want to be here,” he said. “He expressed to me that he’s excited about getting healthy and getting going. And we’re excited about him getting healthy and getting going.”

Reports earlier this week indicated that Kaepernick’s representatives would be meeting with 49ers brass at the combine. Between the positive thoughts expressed by Kelly and Baalke, those talks should start on a far less shaky foundation.