CodeIgniter: Removing index.php from the URL - php

Question

I was trying to remove the index.php from the URL, on my WAMP server THIS worked perfectly, but for some reason on my actual hosted server it's not.
I just created on my current Linux Ubuntu Server a sub-domain,
under /var/www/tools.example.com/public_html
I checked if mod_rewrite is enabled using a .php file I uploaded to the dir with this:
<?php
phpinfo();
and mod_rewrite is under "Loaded Modules".
so no worries here.
the .conf file I created in etc/apache2/sites-available/tools.example.com.conf looks like this:
<VirtualHost *:80>
ServerName tools.example.com
ServerAdmin walid#example.com
ErrorLog /var/www/tools.example.com/logs/error.log
CustomLog /var/www/tools.example.com/logs/access.log combined
DocumentRoot /var/www/tools.example.com/public_html
<Directory /var/www/tools.example.com.conf/public_html/>
Options Indexes FollowSymLinks MultiViews
# changed from None to FileInfo
AllowOverride All
Order allow,deny
allow from all
</Directory>
</VirtualHost>
where AllowOverride All so using mod_rewrite with .htaccess is enabled.
I don't know why this is still not working. Any idea why?
the content of the .htaccess file in the main dir:
RewriteEngine on
RewriteBase /
RewriteCond $1 !^(index.php|resources|robots.txt)
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L,QSA]
Edit #1:
I already went through all first 9 solutions in this post: CodeIgniter removing index.php from url

Answer 1

Your path is incorrect in your .conf file for the directory directive. Your document root listed should be the same as your Directory directive. So I don't think it's picking up the AllowOverride All directive.
Change this
<Directory /var/www/tools.example.com.conf/public_html/>
To this
<Directory /var/www/tools.example.com/public_html/>