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I also remember he wrote something about modders not trying to implement something new, but only each making their own scripts, which seemed not quality to him. This makes sense since as I understand you plan to move those scripts to your game. And also if i'm right he considered PotC engine flawed very much?

There are no scripts that could be moved from the mod to the new game. Plus, it wouldn't make sense as the mod was working within the constraints of the Akella engine and the new game is free of that, so we can build the classes and method as we see fit, without needing to work around their architecture. Other than following the same basic pattern of the mod there isn't anything really that can be salvaged other than some user assets.