But if you are still go for this normal structural programming and want to manage the files, then see how I would go for:
- all the PHP/HTML files that are accessed from URL (browser's address bar) i.e. index.php, about.php, etc.
- all the including files like header.php, footer.php, left.php (which are included in the main files index.php, about.php, contact.php)
- all the images
- all css files
- all the PHP files that are not directly accessed from browser but included instead i.e. functions.php. Also all the third party codes/classes i.e. fpdf, phpmailer, etc.
- all the classes that you developed if you have any (just to segregate from other include files.
I don't say best one but would cover and show the difference of the files