The No Specializations mod broke with 1.01, the first 2 options now show up in tree view. Loading my save game is allowing me to research specializations I had already taken again because it now places the first two options from each specialization are now added to the tree. For a new game this can still work out if you always take the third option. I'm also thinking that removing the specialization restrictions would work better but haven't started looking at that yet. I read in another post somewhere or heard on the stream that the extreme worlds restriction was removed, if so there should be a way to just remove the restriction but again I haven't looked at it yet.
Yeah, 1.01 has done something odd with then. I could only select the extra specs in the tree, which doesn't show the 3rd spec.
However, if you select one of the new specs, the other ones also appear (but for some reason, only the new specs). So it still works, to an extent.
Unfortunately, I have no idea why the issue is happening. Everything seems the same in the XML. Nothing I can do about it at the moment
The best bet is for someone to make a complete re-do of the specialisations. I don't have the time right now to do that, and then to update it every time the game updates.
Create a new tech that replaces the specialisation. Make the tech that comes after the specialisation instead only require this new tech. THEN you can remove the specialisation tags.