Of course, this is just some freeware that you can download. The only change is that the Linkage page and the Linkage Download page all download version 3, not the old version 2. There is no way to get Linkage 2 anymore.
No one reported any bug in version 3, so it is seems good enough to use. I have still not had a chance to make more interesting geared mechanisms, but that will come with time.
I am also still working on a Linkage mechanism page to show GIF animation of mechanisms as well as have links to their .linkage2 files. I hope to get that working soon, but getting good GIF animations is harder than I thought.