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Unfortunately, the Turkish translation by Adnan CEMGİL is still in copyright, so I have deleted the link from your post.
More unfortunately, an automatic conversion from PDF to a Mobi with footnotes is not possible. You'll have to take what output you can get and manually fix up the footnotes. I'd suggest conversion to HTML or ePub first, clean that up with a text editor, and then only convert to mobi when you're happy with it.
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