New to DRUPAL, Debian 8, apache2, MariaDB, PHP 7.x, DRUPAL 8, localhost, not published yet.
This problem of no clear URLs appeared out of nowhere as clear URL worked perfectly for few weeks.
I DID change the site name, I guess just for the sake ot it, a day before to use ngrok and see if at friend's place I could see my site.
Well there was this weird problem: The front page (with ngrok using IP only) was ok but other links were not found cause there was index.php inserted in front of the link. Manually removing the 'index.php' part worked ok.