I noticed while looking at 29er frames and trying to sort out the correct size that top tube seem to all have gain about 1/2 inch. Is this because we are supposed the be running much shorter stems?

Kind of. It’s more to do with moving the front centre (aka front axle) back to the same place it’s in with a 26er with similar steering feel, due to the 29er having a steeper head angle. Neatly explained here (scroll down to development): http://www.cotic.co.uk/product/solaris

I went down a size as it was a rigid SS so unlikely to be used for much more than winter messing about in the woods so all day stretched out comfort wasn’t a problem.