Why are sub-directories not found
<p>I have been looking at other answers here on stackoverflow and elsewhere, to no avail. </p>

<p>I am running a virtual-host localhost and the homepage of the site is showing up fine, but if I go to any subdirectory/subpage I see this error:</p>

<blockquote>
  <p>The requested URL /downloads/ was not found on this server</p>
</blockquote>

<p>In sum, <strong>mydomain.com</strong> works, but <strong>mydomain.com/downloads/</strong> does not work.</p>

<p>Usually I have fixed this issue with other domains on my localhost by altering <code>.htaccess</code>. Here is my current setup:</p>

<p><strong>Apache2.conf</strong></p>



<pre class="lang-bash prettyprint-override"><code>&lt;Directory /&gt;
    Options FollowSymLinks
    AllowOverride None
    Require all denied
&lt;/Directory&gt;

&lt;Directory /usr/share&gt;
    AllowOverride None
    Require all granted
&lt;/Directory&gt;

&lt;Directory /var/www/&gt;
    Options Indexes FollowSymLinks
    AllowOverride None
    Require all granted
&lt;/Directory&gt;
</code></pre>

<p><strong>mydomain.com.lc.conf</strong> in <strong>sites-available</strong></p>

<pre class="lang-bash prettyprint-override"><code>    &lt;VirtualHost *:80&gt;
        ServerName mydomain.com.lc
        ServerAlias www.mydomain.com.lc
        ServerAdmin myemail@mydomain.com
        DocumentRoot /var/www/html/mydomain.com.lc/com_mydomain/
        SetEnv APPLICATION_ENV local
        &lt;Directory /var/www/html/mydomain.com.lc/com_mydomain &gt;
                Options Indexes FollowSymLinks MultiViews
                AllowOverride all
                Require all granted
        &lt;/Directory&gt;
    &lt;Directory /var/www/var/www/html/mydomain.com.lc/com_mydomain/*&gt;
        Allow from all
        Deny from none
        Order deny,allow
    &lt;/Directory&gt;

        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined
&lt;/VirtualHost&gt;
</code></pre>

<p><strong>000-default.conf</strong></p>

<pre class="lang-bash prettyprint-override"><code>&lt;VirtualHost *:80&gt;
    ServerAdmin webmaster@localhost
    DocumentRoot /var/www/html
    ErrorLog ${APACHE_LOG_DIR}/error.log
    CustomLog ${APACHE_LOG_DIR}/access.log combined
&lt;/VirtualHost&gt;
</code></pre>

<p><strong>etc/hosts</strong></p>

<pre class="lang-bash prettyprint-override"><code>127.0.0.1   mydomain.com.lc
</code></pre>

<p><strong>.htaccess</strong></p>

<pre class="lang-bash prettyprint-override"><code>Options +FollowSymLinks

RewriteEngine On

RewriteBase /

&lt;IfModule mod_rewrite.c&gt;    
 RewriteEngine On 
 RewriteBase / 
 RewriteRule ^index\.php$ - [L] 
 RewriteCond %{REQUEST_FILENAME} !-f 
 RewriteCond %{REQUEST_FILENAME} !-d 
 RewriteRule . /index.php [L] 
&lt;/IfModule&gt;
</code></pre>

<p>I've tried using no <code>.htaccess</code> as well.</p>