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Alex Smith, San Francisco 49ers make a new deal

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Best buddies again? It would appear to be so. (Getty Images)

After the 49ers' dalliances with Peyton Manning, and quarterback Alex Smith's corresponding free-agent visit to Miami, it seems that both sides have agreed to make nice ... and make do. Matt Maiocco of CSN Bay Area confirmed a report from Michael Lombardi of the NFL Network, indicating that the 49ers have re-signed Smith. Before 49ers head coach Jim Harbaugh and offensive coordinator Greg Roman flew to North Carolina last Tuesday to watch Manning work out, Smith had been considering a three-year, $24 million offer from the team.

Because Smith hadn't yet agreed to terms, the 49ers felt justified in going after Manning, an option that Manning seriously considered before agreeing to terms with the Denver Broncos on a five-year, $96 million deal. The speculation was that Manning wouldn't sign with an NFC team because he might have to face brother Eli in the playoffs, but Manning refuted that claim when asked by the NFL Network's Rich Eisen on Tuesday.

[Related: Tim Tebow's friend says QB wants to head back to Florida]

"It's unfair to say that because I wouldn't have had the discussions and the talks and the workout for the San Francisco 49ers if that were the case," Manning said. "I knew that San Francisco was in the NFC. When the two of us started to talk, I very easily could have seen myself being a 49er. That's why it was so hard. I kept wanting for someone to just tell me where to go."

Once John Elway told Manning where to go, it was left for Harbaugh and the 49ers organization to clear up any miscommunication and hard feelings with Smith. Reports indicated that while Smith understood the team's pursuit of Manning, he was less than happy to learn of Manning's throwing session with team officials just before the news of that workout broke. In addition, Smith may be at his wit's end with agent Tom Condon, who's been rather busy representing that very same Peyton Manning fellow recently.

[Related: Alex Smith must swallow pride after Peyton Manning pursuit]

On Monday, 49ers CEO Jed York said that the three-year deal could still be signed. "We have a contract on the table and it's up to him," York said. "We'd like for him to be here, and we'll see where it goes."

The Sacramento Bee reported that Harbaugh and Smith met for an hour on Monday to try and get everything smoothed out.

Smith, who threw just five regular-season interceptions in 2011 in a career year, helped the 49ers to a 13-3 record and a near-Super Bowl berth. Harbaugh was the key to his professional rebirth after six disappointing seasons. But the 49ers' dance with Manning had Smith on a plane to Miami last Saturday, where he met with team officials and coaches for 5 1/2 hours. He was also considering an offer to visit the Seattle Seahawks before they pulled the trigger on a three-year, $26 million deal with former Green Bay Packers quarterback Matt Flynn.

In the end, the Dolphins signed ex-Jacksonville Jaguars quarterback David Garrard to a one-year deal, and Smith headed back home.

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