Automatic base uri detection.
define these constants on top of your public/index.php
// setup constants
if (!defined('DS')) {
    define('DS', DIRECTORY_SEPARATOR);
}
if (!defined('ROOTFULLPATH')) {
    define('ROOTFULLPATH', dirname(__DIR__));// if this file is under /public, up one level.
}
if (!defined('APPFULLPATH')) {
    define('APPFULLPATH', ROOTFULLPATH.DS.'app');
}
add MyConfig class in app/config/config.php file and call to getBaseUri().
<?php
class MyConfig extends \Phalcon\Config
{
    public function getBaseUri()
    {
        $replaced_slash_fullpath = str_replace('\\', '/', ROOTFULLPATH);
        $request_uri_no_slash_trail = rtrim($_SERVER["REQUEST_URI"], '/');
        return $this->findMatchUri($replaced_slash_fullpath, $request_uri_no_slash_trail);
    }
    private function findMatchUri($str1 = '', $str2 = '')
    {
        if (strpos($str1, '/') === false || strpos($str2, '/') === false) {
            return '/';
        }
        $str1_arr = explode('/', $str1);
        $str2_arr = explode('/', $str2);
        $found_matched = [];
        foreach ($str1_arr as $uri_target) {
            foreach ($str2_arr as $uri_find) {
                if (strcmp($uri_find, $uri_target) === 0) {
                    $found_matched[] = $uri_find;
                }
            }
        }
        unset($str1_arr, $str2_arr);
        if (empty($found_matched)) {
            $found_matched_string = '/';
        } else {
            $found_matched_string = '/'.implode('/', $found_matched).'/';
        }
        unset($found_matched);
        return $found_matched_string;
    }// findMatchUri
}
$myconfig = new MyConfig();
$auto_base_uri = $myconfig->getBaseUri();
unset($myconfig);
return new \Phalcon\Config(array(
    'database' => array(
        'adapter'     => 'Mysql',
        'host'        => 'localhost',
        'username'    => 'admin',
        'password'    => 'pass',
        'dbname'      => 'test',
        'charset'     => 'utf8',
    ),
    'application' => array(
        'controllersDir' => __DIR__ . '/../../app/controllers/',
        'modelsDir'      => __DIR__ . '/../../app/models/',
        'viewsDir'       => __DIR__ . '/../../app/views/',
        'pluginsDir'     => __DIR__ . '/../../app/plugins/',
        'libraryDir'     => __DIR__ . '/../../app/library/',
        'cacheDir'       => __DIR__ . '/../../app/cache/',
        'baseUri'        => $auto_base_uri,
    )
));