Can I put my WordPress theme files in another folder?
The answer is yes. Like @Kvvaradha mentioned in his comments. If you put header.php footer.php index.php functions.php style.css must be in /wp-content/themes/your-theme-folder. And other your library, components and includes could be put anywhere that you prefer. But, make sure files and folders structure are flexible. Good luck in your codes 🙂