Here is a way to replace wordpress files with known good copies.
Download WordPress files from GitHub repository
The wp-content folder and the wp-config.php file are the only unique items in wordpress. (with the exception of domain verification files.) It contains media, plugins, and themes. Download a fresh copy of the WordPress files from the GitHub repository.
Download files
git clone https://github.com/WordPress/WordPress
Remove the wp-content directory from the WordPress directory
rm -rf WordPress/wp-content
Copy the wp-config.php file from html directory to the new WordPress directory
cp -a html/wp-config.php WordPress/
Copy the wp-contents dir from the html directory to the new WordPress directory
cp -a html/wp-content WordPress/
Swap the html directory with the WordPress directory
mv html html.old; mv WordPress html
Update permissions on new html directory
cd html; nkwordpress -op .