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I am using Microsoft’s IIS SEO analyzer, and it keeps showing me a warning that I have a canonical link error because I’m storing the same file in different folders on the server. Doing this makes my file structure much more organized that linking different folders together. Should I just ignore this or is this a big deal for SEO?
Where files are located on your server has nothing to do with SEO. There is no way for search engines to know where files are actually located and a page’s URL dos not necessarily indicate its location on the server. What does matter is whether two URLs pull up the same page. That would be duplicate content and a problem for your SEO efforts.