To answer your question Privateer, I don't think it is nessisary or even a good idea to try to keep all the MODs from breaking the game. I think that MODs in the centralized list should be tested before being added. Anything else would be marked experimental and the program would state that it can't be garanteed not to break things.
As for a MOD breaking someone else's MOD... I think that will always be a possiblity, though having each one only edit what it is changing would certainly cut down on this. Before applying a MOD, the program should check that no other ones have changed the same variable and alert you with an optional list of all conflicts. This could even be an option for MOD devs to click and check against all currently downloaded content. Having a centralized program that tracks only the changes a MOD makes and lets you edit any variable quickly and fairly easily should make testing and resolving conflicts much easier, yes?
I realize that at times one person might edit for example the wave height or such and that may not conflict with another MOD's changes but could still cause odd behavior. This is simply a risk that each person takes with an experimental MOD or personal changes.
We could impliment a 'Risky Changes' section in the MOD files that details what variables are known to be dangerous to change that would red flag with the conflicts. These could be taken from an internal listing compiled as we use the tool.
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