WordPress Skeleton, VVV, Multisite, and the right Nginx rules

Just few notes:

Your wp-content/ folder isn't under the wp/ folder as you stated here:

rewrite ^/(wp-(content|admin|includes).*) /wp/$1 last;

Since default themes, like Twenty Fifteen come shipped with the /wp/wp-content/ folder, it could explain why you get it to work there.

Regarding the missing /wp/ part in the network admin urls, Daniel Bachhuber has posted this handy gist snippet that fixes that problem. It uses the network_site_url filter to inject it.

<?php/** * Fix network admin URL to include the "/wp/" base *  * @see https://core.trac.wordpress.org/ticket/23221 */add_filter( 'network_site_url', function( $url, $path, $scheme ){    $urls_to_fix = array(        '/wp-admin/network/',        '/wp-login.php',        '/wp-activate.php',        '/wp-signup.php',        );    foreach( $urls_to_fix as $maybe_fix_url ) {        $fixed_wp_url = '/wp' . $maybe_fix_url;        if ( false !== stripos( $url, $maybe_fix_url )            && false === stripos( $url, $fixed_wp_url ) ) {            $url = str_replace( $maybe_fix_url, $fixed_wp_url, $url );        }    }    return $url;}, 10, 3 );

Also see the open ticket #23221 on Multisite in subdirectory with root site address

Some discussions here on GitHub regarding nginx + multisite with wp-skeleton structure (I posted there some experiments some time ago).

Consider a solution just with updated NGINX config, which I've published on github.Change your rewrites with following

if (!-e $request_filename) {   rewrite ^/(wp-admin/.*)$ /wp/$1 last;   rewrite ^/[_0-9a-zA-Z-]+(/wp-admin/.*)$ /wp/$1 last;   rewrite /wp-admin$ $scheme://$host$uri/ permanent;   rewrite ^/[_0-9a-zA-Z-]+(/wp-includes/.*) /wp/$1 last;   rewrite ^/(wp-[^/]+\.php)$ /wp/$1 last;   rewrite ^/[_0-9a-zA-Z-]+(/wp-.*) $1 last;   rewrite ^/[_0-9a-zA-Z-]+(/.*\.php)$ $1 last;}rewrite ^/(wp-includes/.*)$ /wp/$1 last;

That will solve all the problems with access to admin panels and the network admin panel with sub-folder installation of the Wordpress Multisite. No need code writing.