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I was also thinking of manually saving the game so we don't have more
than one save file in the repository at a time. The folder it is
currently in is where the game saves when you press enter. I thought it
would be easier for it to be automatic, but it is messier because the
game doesn't overwrite the previous file; it creates a new one.
I cut the civ4game folder and pasted it one directory up. The folder is
now in the saves folder sitting right next to the
pebm,hotseat,single,multi, and so on folders.
I saved the game as ourSavedGame, and when github came up, I had to tell
it where the civ4game folder was again.
Just do that and overwrite the saved game there, and it should be much
simpler.
If theres a problem, just send me an email.