What is meant by extend an offer in this context?

Context: I applied online on a job posting site and had a phone interview with the manager of my field. These emails happened next.

Manager: I would like to extend the internship to you from beginning date to end date. Please let me know if you accept or not so then I can contact you with HR.”

Me: I accepted.....(more text formally didn’t want to type it all out)

Manager: welcomes me to organization.

HR: emails me saying the position just opened and to apply again but on the the organizations site to proceed to next step of hiring.

I’m confused why am I applying again? Did I not get the position and I have another screening?

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