Remove subfolders from URL

You need to make the WP site url and home url differ in Settings / General. The home url should be example.com, while the site url (where WP lives) should be example.com/wp (or wherever you put it).

You can hardcode these in your config file:

define('WP_HOME',    'http://example.com');
define('WP_SITEURL', 'http://example.com/wp');

WP should know how to take things from there, and place the .htaccess where it should be.

In case it doesn’t, my own site’s folder looks like this:

• .htaccess
• index.php
• wp

The index.php file contains:

<?php
// WordPress view bootstrapper
define( 'WP_USE_THEMES', true );
require( './wp/wp-blog-header.php' );

And the .htaccess contains:

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

Regarding the /index.php bit in URLs generated by WP, it means WP is (incorrectly?) finding that your site cannot manage permalinks. (Can I wager that this is because you’re using Nginx?)

Assuming you know better than WP, add a must-use plugin in your wp-content/mu-plugins folder, e.g. a force-permalinks.php file:

<?php
add_filter( 'got_rewrite', '__return_true' );