The San Francisco 49ers had two major goals to accomplish this offseason.

They are halfway to accomplishing them.

The 49ers signed quarterback Colin Kaepernick to a lucrative contract extension through the 2020 season on Wednesday. Kaepernick was entering the final year of his contract. Now, the 49ers have to complete their immediate task of securing a strong future by extending the contract of coach Jim Harbaugh.

Jim Harbaugh and Colin Kaepernick have had plenty to smile about in recent seasons. AP Photo/Ben Margot

Harbaugh is entering the fourth year of a five-year contract that will pay him $25 million. Harbaugh has led the 49ers to three NFC Championship Games and one Super Bowl appearance in his three seasons as an NFL head coach.

Harbaugh is the third highest-paid coach in the NFC West.

In the long run, the value of the Kaepernick deal will not mean as much if Harbaugh isn’t working with the quarterback.

These two are a package deal.

It was Harbaugh who identified Kaepernick as a future franchise quarterback out of Nevada and convinced the 49ers to trade up and take him in the second round of the 2011 draft.

A former NFL quarterback himself, Harbaugh’s coaching is inspired by Kaepernick’s unique skill set. Harbaugh is giddy when he talks about his quarterback. A familiar scene after 49ers games is the two embracing in the locker room after another San Francisco win. At the news conference to announce his new deal Wednesday, Kaepernick acknowledged his coach’s influence multiple times.

These two have already enjoyed major success together as Kaepernick is 21-8 in his 29 NFL starts. The future is boundless.

But Harbaugh has to be a part of it, and there are no guarantees that will happen. The 49ers and Harbaugh have talked about an extension since last year.

Both sides are open to a deal, but they don’t appear to be close. There has been a lot of talk that Harbaugh wants to average in the $7-8 million range. But the 49ers are reluctant to pay him like a Super Bowl-winning coach until he actually wins a Super Bowl.

We all know the reports of a rift between Harbaugh and 49ers management. All parties have said those reports have been overblown, and while there is some competitive tension in the building, Harbaugh works well with others, including general manager Trent Baalke.

The truth is, the 49ers have won with Harbaugh, and the team had a productive offseason even after the reported interest by the Cleveland Browns to trade for Harbaugh.

If the 49ers doesn’t extend Harbaugh's contract before next January, expect more reports of teams being interested in making Harbaugh their coach. If the 49ers enter the final year without a new deal for Harbaugh, the odds of such a trade could increase.

That would not be in the best interest of the team and Kaepernick. The 49ers made great strides in getting the Kaepernick deal done. Now, it’s time to secure the man he is most connected to in the organization.