DotSpatial has changed their repository structure to have a new level of folders, this breaks the MapWindow6 solution.
I fixed this for myself by opening MapWindow.sln and changing each of the five DotSpatial project locations from something like this:
to something like this:
I also needed to change the DotSpatial library references in the MapWindow6 project to CopyLocal=True.
Now MW6 is happily running in debug mode with the latest source code from both projects.