If you register a taxonomy named projects, and create taxonomy-projects.php, the URL mysite.com/projects will not exist. There is no such page in WordPress.
If you create a term inside inside that taxonomy, “My Project”, that term will be accessible at mysite.com/projects/my-project and that URL will use taxonomy-projects.php to list all posts that belong to that project. mysite.com/projects on its own does not exist.
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