Mod rewrite enabled and working, urls contain index.php/ I have a strange issue: I have a drupal 8 instance on a subfolder in /var/www, I have enabled mod-rewrite in apache, I changed the apache.config file as in this post and the clean urls are working if I navigate directly to /drupal/admin for example.

I also added the RewriteBase /drupal in my .htaccess file.

The problem is that any link generated by drupal still contains the /drupal/index.php/ part and I don't know how to get rid of that /index.php part.

I worked with Drupal 7 since it was launched but I never had this problem. 

Is there a setting somewhere in db or in the config file where I should 'tell' drupal to use clean urls?

My server runs Apache 2.4.7 and PHP 5.5. 

Thank you.
If you didn't append /index.php to the base URL (e.g. setting $base_url to http://example.com/index.php, in the settings.php file), then the rewrite rules in the Apache configuration files are wrongly adding /index.php to your links.
Check both of them, and you should find what is causing the wrong behavior.