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Codeigniter3 EC2 remove index.php

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I have an EC2 instance running Ubuntu 16.04. I have installed a LAMP stack and am using Codeigniter.
the removal of index.php is not working as it should. I can reach the first page but if I click on any links in the page it does not work.
I have tried to follow the directions here: CodeIgniter removing index.php from url but, It has not helped

I have tried to edit the apache2.conf to allow override but this gives an error all the time.

I have tried almost every post online.

.htaccess file: (original)
Code:
RewriteCond $1 !^(index\.php|assets|images|js|css|uploads|favicon.png)
RewriteCond %(REQUEST_FILENAME) !-f
RewriteCond %(REQUEST_FILENAME) !-d
RewriteRule ^(.*)$ index.php?/$1 [L,QSA]

config.php:
Code:
$config['index_page'] = '';
$config['uri_protocol']    = 'REQUEST_URI';

header.php:
Code:
<li><a href="<?php echo base_url(); ?>">Home</a></li>
       <li><a href="<?php echo base_url(); ?>about">About</a></li>
       <li><a href="<?php echo base_url(); ?>pricing">Pricing</a></li>

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