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The file on the first page is an ips file, it is used to patch the original ruby rom to change it to snakewood. You need to download a clean ruby rom and patch it using that file, it will then be able to be read by visual boy advance.
So I was looking for sundance rock in solar caverns, and the i observed the lake, it said there was something under the water so I jumped in. I then saved the game, but soon after I realized I was in that submarine thing with that guy and the elevator and the magnemite and all of that. Thing is...