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Some questions don't have tags. So how do "Related questions" are picked for these no-tag questions ?

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Based on the question title and (if available) the question category. See function qa_db_related_qs_selectspec() in qa-db-selects.php for the query.

How do we remove some words like "how, what and ..." from qa_db_related_qs_selectspec() function?
Yes, these common words are really making related questions a mess. If we have tags then users will post inaccurate (common words ) tags there too. Related questions is very important for a broad niche or general category SEO.