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Originally written by Thuryl: I'm almost certain that save files will be incompatible.
Why? It doesn't make any sense to change the file format when porting the game. You're not storing any more or less information in save game files. They're also binary, so the Mac vs. Unix vs. Windows newline characters don't change anything.
Speaking as a professional programmer: ideally (in a well-designed program), you only need to change the code that interacts with the OS APIs. This can include drawing graphics, playing sound, storing preferences, etc. The backend should be totally platform-independent. In an object-oriented language, you'll only need to swap out a few classes to make this work. I don't see why it's taking Jeff so long to port BoA to Windows, seeing as he already has the Avernum engine written for Windows.