After encouragement from Stillwater officials the Minnesota legislature has approved funding for the Browns Creek Trail that will connect the Gateway Trail to downtown Stillwater over the 6.5 mile former Minnesota Zepher line. The first article I've seen was published by the Stillwater Gazette. Brown's Creek Trail will, like the Gateway Trail, be a segment of the Willard Munger State Trail.
It looks like construction will start this year and be completed next year.
You can see where the trail will go by going to Cyclopath.org and searching for "Brown's Creek".
I really enjoy riding to Stillwater and this project will make the trip so much easier with very few conflict points and a very gradual grade back up from the river. The folks in Stillwater seem excited too; there will be more tourists but not more cars on the very congested highway through downtown.