Remove uploads folder & images.

Move source images to /assets, and ignore uploads.
Remove & ignore .gitattributes file
Remove duplicate style.css
Remove shortcodes.php

If we want to create any shortcodes, they should be in a plugin, not the theme. This way, if/when we change the theme, we don’t loose the shortcodes.
Remove layouts CSS folder

This is a vanilla-css duplicate of sass/layouts, and is not used.
Update the Theme Header
Remove ending PHP tag

This is a best practices/code standards thing, see https://make.wordpress.org/core/handbook/coding-standards/php/#remove-trailing-spaces