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Well, in quite a few cases they don't. For example, I've seen the file structures for quite a few 3DS games via the modding community, and the files are often just named complete gibberish. Like 'file1music.brr' to 'file2639music.brr'.

But from games which do have somewhat logical structures, it's usually that the files are seperated by purpose. So the music and sound effects in one folder, the textures in another, some level files in another folder, etc. And the names would be somewhat descriptive of the content, like 'course_desert_1.lvl' If you're lucky, this is also backed up in a git repository somewhere and has version control.

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