When Will The Expansion Be Coming Out?
In all likelihood, October.
Hurray! I have a date for when I can make you take my money!
Of course, you all realize that come October 1st, you'll be subjected to an endless stream of "Is it ready yet?" posts?
Historically speaking permadeath options don't include protection against the player messing with the filesystem. So all the game has to do is not autosave and immediately quit back to the main menu after any manual save (edit: and delete the manual save file immediately after loading it)
Well, if you wish to prevent file system fiddling, as it was said yesterday, that's fairly simple. Whenever a new game is started, generate a new encryption key. Whenever a save is made, encrypt it with the key generated for that game. When the game is lost, delete the key from your central "active games" repository, which would make it impossible to decrypt any copies of the saved games that may have been created.
Of course, that leaves your central repository vulnerable to external modification, so it would need to be encrypted as well.
To prevent the repository from being copied and restored, you could re-encrypt the repository with a different key each time, using a generated key based upon a seed, randomly generated during the initial AI War installation. This does potentially leave open attacks based on the nth-save/n-th seed pairing, though.
This still leaves you vulnerable to people backing up and restoring the entire AI War installation, so you'd need to secretly install an invisible rootkit service that would prevent access to the repository except through authorized programs.
Of course, that could be gotten around if the user installs AI War into a Virtual Machine, and restores to a previous snapshot when a game is lost.
In that case, I'm afraid the user wins. (Wins what? At this point, I'm not sure)
In which case, it all comes back to the very beginning - If the user is really determined, they could just turn off permadeath mode. Thus, I'm not sure why any real effort would need to go into creating a perfect permadeath mode to begin with.