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/usr/bin/apigen is in php-apigen 4.1.2-1ubuntu2.

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The actual contents of the file can be viewed below.

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#!/usr/bin/php
<?php

require 'ApiGen/autoload.php';


// Create temp dir
$tempDir = sys_get_temp_dir() . '/_apigen';
ApiGen\FileSystem\FileSystem::purgeDir($tempDir);


// Init debugger
Tracy\Debugger::$strictMode = TRUE;
if (isset($_SERVER['argv']) && ($tmp = array_search('--debug', $_SERVER['argv'], TRUE))) {
	Tracy\Debugger::enable(Tracy\Debugger::DEVELOPMENT);

} else {
	Tracy\Debugger::enable(Tracy\Debugger::PRODUCTION);
	Tracy\Debugger::$onFatalError[] = function() use ($tempDir) {
		echo "For more information turn on the debug mode using the --debug option.\n";
		ApiGen\FileSystem\FileSystem::deleteDir($tempDir);
	};
}


$configurator = new Nette\Configurator;
$configurator->setDebugMode( ! Tracy\Debugger::$productionMode);
$configurator->setTempDirectory($tempDir);
$configurator->addConfig(__DIR__ . '/../share/php/ApiGen/DI/config.neon');
$configurator->addParameters(['rootDir' => __DIR__ . '/../share/php/data/ApiGen']);
$container = $configurator->createContainer();


/** @var ApiGen\Console\Application $application */
$application = $container->getByType('ApiGen\Console\Application');
$application->run();


// Remove temp data
ApiGen\FileSystem\FileSystem::deleteDir($tempDir);