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Simple question: If I use a spob resource in my plug that is already used in the data files of EV Nova, will whatever I change on that resource override the data file resource?
Another way to say this is that I want to make a plug-in that changes some things regarding a pre-existing planet, would I just make a spob resource in my plug-in with the same ID as the spob resource of the planet I want to change in the data files and make my changes?
Yes, this is exactly how resources work (and not just in the Escape Velocity games, either). If more than one open file contains (for example) a spöb resource of ID 128, the last one loaded is used, and the other copies are simply ignored. If you want to replace any of the resources from the original game whether with slightly modified versions, or with something entirely new this is the way you do it.
The order the data files load is this: files in the Nova Data folder in alphabetical order, then files in the Nova Plug-Ins folder, in alphabetical order.
Note that an interesting side-effect of this is that placing a plugin in the Nova Data folder will have the same effect as placing it in the Nova Plug-Ins folder, save that it may come at a different point in the load order.
The main advantage of the nova plugins folder is that you can "overwrite" files in the nova data folder without harming them.