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For someone who had never done any serious coding prior to this project, I quickly discovered I had my work cut out for me and needed to learn a lot quickly.
One of the subjects that was a true challenge was determining if an email from a user was a reply to a current thread, or if it was starting a whole new thread. I accomplished this by adding a reference to the email headers when the email was sent out.
Then when the cron job ran and checked the email box, it checked each email for those references and if it found, it would cut it apart to retrieve the threadid. If the reference didn't exist, the script figured out it was likely a forwarded email to the list, and processed it as a new thread.