It offered to when I started up but I clicked cancel so I could go commit changes and make a branch. When I came back it did not offer it again.
My app has a watch extension and a today extension.
How do I run the project migration on an old project?
Well, first thing...and sorry to say this: XCode will not automatically 'port your Apple Watch code. All you really have to do is create new apple watch target. XCode will do that for you and then you must copy all your code and xib's, assets, storyboards yourself.
Apple says this in their transition to watchos2 document.
(Sorry, i don't know how to reactivate migration assistant but this is the answer you will end up with anyway...migration really isn't migration with XC7)