Well, the trade window has closed for the season. But, and in this regard John Lynch may be smarter than given credit for, SF signed Jones to a two-year deal, without an out for Mac after this season. Also, he'll get paid $4m next season, but if SF cuts him (or another team does a trade/cut, unlikely but possible), the dead cap is only a little over $2m, making him really easy to deal next off-season, if they want. Or they can just hold onto him as insurance at a reasonable cost.
This was really damn smart because they saw: Jones has talent, but went through a really bad coaching carousel his entire career so far. So he was always between decent and bad, depending on the week. He best play was for a smart OC who works with QBs in Josh McDaniels, and he had a few moments his year in Jax, but that whole org was a mess. "But in a stable system like ours, where I, QB whisperer Kyle Shananhan actually work with my QBs and coach to their strength, unlike other idiot coaches out there..." they grabbed him at a very reasonable cost, and can hold him for two seasons. They saw what worked with Darnold, but lost Sam after 1 season (as did Minnesota). So Lynch got the "damaged" Jones to sign a 2-year deal.