Apps_paths are blocking nextcloud upgrade

ℹ️ Support
1

Nextcloud version 11.0.2
Operating system and version Ubuntu 16.04
Nginx version 1.10.0-0ubuntu0.16.04.4
PHP version 7.0.13

I created an apps_paths as followed, /srv/www/nextcloud being the root of the NextCloud install :

$CONFIG = array (
[...]
'apps_paths' => 
  array (
    0 => 
    array (
      'path' => '/srv/www/nextcloud/apps',
      'url' => '/apps',
      'writable' => false,
    ),
    1 => 
    array (
      'path' => '/srv/www/nextcloud/apps.installed',
      'url' => '/apps.installed',
      'writable' => true,
    ),
    2 => 
    array (
      'path' => '/srv/www/nextcloud/apps.manual',
      'url' => '/apps.manual',
      'writable' => false,
    ),
[...]
);

When launching an upgrade to 11.0.3, it stops quickly with this error:

Check for expected files
The following extra files have been found:
apps.manual
apps.installed

I was expecting that it would allow those path because they are configured. How can I workaround this weird behavior ? Also app_paths have to be in nextcloud webroot in order to have static assets loaded.