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Run Magento 2 commands programatically 

<?php

use Magento\Framework\App\Bootstrap;
require __DIR__ . '/app/bootstrap.php';
$bootstrap = Bootstrap::create(BP, $_SERVER);
$obj = $bootstrap->getObjectManager();
$state = $obj->get('Magento\Framework\App\State');
$state->setAreaCode('frontend');
$k[0]='bin/magento';
$k[1]='cache:flush'; 
// write your proper command like setup:upgrade,cache:enable etc...
$_SERVER['argv']=$k;
try {    
    $handler = new \Magento\Framework\App\ErrorHandler();    
    set_error_handler([$handler, 'handler']);    
    $application = new Magento\Framework\Console\Cli('Magento CLI');    
    $application->run();
} catch (\Exception $e) {    
   while ($e) {        
      echo $e->getMessage();        
      echo $e->getTraceAsString();        
      echo "\n\n";        
      $e = $e->getPrevious();    
   }
}
?>

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