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Threading is first attempted using the references on the message provided by the "References" or "In-Reply-To" headers, in that order. For each reference (starting from the last reference and working towards the first), an attempt is made to either a) locate the message with either the given Message-ID, or b) (if mail.correct_threading) locate a sibling message that references the same Message-ID.

If the References/In-Reply-To doesn't pan out and the "mail.strict_threading" preference is False, then the subject is potentially used for threading. If the "mail.thread_without_re" preference is True (default), then the subject is used regardless of whether "Re:" is present. If it is False, then "Re:" or a variant must be present. The "Re:" checking is actually fairly thorough; NS_MsgStripRE allows for all case-variants plus "Re[#]:" variants. Additionally, the preference "mailnews.localizedRe" is used to provide a comma-delimited list of alternative prefixes that are allowed. bug 319037 enhances things to use the locale's region.properties to provide this value.

If a thread still hasn't been determined, and the "mail.correct_threading" preference is true, the code will check if the message is an ancestor of an already-threaded message. Because this comes after the subject-threading, it implies that if you enable mail.correct_threading, you will also want to enable mail.strict_threading.

Finally, if a thread still hasn't been found, a new thread is created.