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EA uses C++ for the game engine (you pretty much need to know C++ as a pre-requisit to take a course on game programming)
The game engine has its own source code which is the exported into an executable program, then it grabs resources from all those other files you see in your EA folder, it uses its own method to decode the 3d mesh file (locations of vertices that make up planes) and the other file type I think is texture assignments. I special version of a 3d modeling program is used to take a source file and edit it, then it is exported to what is in you game files folder and those can be decoded by the engine.
The devs like Jason Lee, Armaggeddon, Telos, and Alien all have special versions of the game that allow them to edit server side stuff like quest databases etc, you can tell this is server side because this engine has the ability to update that stuff mid game.
To edit the larger files like game engine properties, including weapon fire rates, projectiles, damage, etc are in some files stored in you endless ages folder, again decoded only by the special programs given to the devs to edit them (and some GMs)
All of these are separate files and not one big file because it saves bandwidth when updating them, so you only have to update parts and not replace the entire program because re-installing every time gets annoying and takes longer. These separate files also reduce memory usage because your computer doesn't have to cache the entire game to ram, just the world you are in and the game engine properties.
*This is not fact, this is me using very educated guess and background knowledge*
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