you dont need any other than the public_html folder, they aren't hurting anything being in different locations to my knowledge, but they are just useless.
If the paths are correct and the yahoo spider is still going insane, try to run your robots.txt thru a robots.txt generator or checker (many available free online) to make sure there are no errors.
After that, i dont have a clue of why Yahoo isn't picking it up.
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