Hi Thunderbrd, I have tested the captured city production bug again as you posted this update in the SVN thread:
8707 -Fixes MAJOR bug with city capturing.
I found it was a partial success. The Stone Tools Maker in a captured city now shows the production values based on my own tech instead of that of the previous owner. I also tested it by almost researching a tech that gives +1 hammer, save the game, and capture a city after researching and not researching that tech. In the former case the captured stone tools maker gives 1 more hammer than the latter, and is consistent with my own cities. Well done!
However, the ghost production bug still exists. A captured city still has more production of every kind than it should, and this vanishes on a forced recalc.
Regarding the question whether it is double summing or starting the calculation with a non-zero baseline, I guess it is a non-zero baseline, because after deleting all buildings with CTRL-A I still have too much production. A captured city with no buildings (all deleted with CTRL-A), no wonders, +2 hammers from tile, and +1 hammer from herd, erroneously totaled 11 hammers base production instead of the expected 3 hammers.