How do I fix permalink and media library issues on a LEMP stack?

Your Nginx website conf should look like that:

location /wordpress {
    try_files $uri $uri/ /wordpress/index.php?$args;
}

This will allow all paths who doesn’t match a real file to be redirected to the index.php with the query sting passed directly to WordPress. WordPress will handle it from there.

More in depth information can be found here: http://wiki.nginx.org/WordPress

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