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On some special days, the crossword puzzles even generate a clever, witty animation that goes along with the hidden theme. In other words, an easter egg.

They're different enough so I could see that they create a separate repository for each special version of the puzzle.

Yeah that’s plausible. And the text is hopefully in some nicely indexed store, a proper database, which references the repos.

That is the case for at least some of the articles. There are also quite a few initialized projects but with nothing inside of them. And the overall file count comes from things like saved email templates that they have sent out, etc. Node modules, and a lot of other garbage files from Terraform, Ansible, etc.