What I generally do
- Install WP in sub directory.
- Open permalink set required permalink.
- Open settings->general link
- Remove the sub directory name from ‘Site Address (URL)’
- Cut the index.php and .htaccess files from sub directory and paste them to root
- change code in index.php as you did.
- Again access settings->permalink save the form
Done. You dont need index.php and .htaccess file in sub directory.
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