https://stackoverflow.com/a/53997599 test case

root@demo:~# ls -l
total 2
drwxr-xr-x 5 root root    8 Jan 10 12:24 36287554
-rw-r--r-- 1 root root 1408 Jan 10 12:27 36287554.php
root@demo:~# ls -l 36287554/
total 3
-rw------- 1 root root 0 Jan 10 12:23 file_a
-rw-r----- 1 root root 0 Jan 10 12:23 file_b
-rw-r--r-- 1 root root 0 Jan 10 12:23 file_c
drwx------ 2 root root 2 Jan 10 12:24 folder_a
drwxrwx--- 2 root root 2 Jan 10 12:24 folder_b
drwxrwxrwx 2 root root 2 Jan 10 12:24 folder_c
root@demo:~# php --version
PHP 5.6.10 (cli) (built: Jan 10 2019 12:07:52)
Copyright (c) 1997-2015 The PHP Group
Zend Engine v2.6.0, Copyright (c) 1998-2015 Zend Technologies
root@demo:~# php 36287554.php
root@demo:~# zipinfo 36287554.zip
Archive:  36287554.zip
Zip file size: 770 bytes, number of entries: 7
drwxr-xr-x  2.0 unx        0 b- stor 19-Jan-10 12:27 36287554/
-rw-------  2.0 unx        0 b- stor 19-Jan-10 12:23 36287554/file_a
drwxrwxrwx  2.0 unx        0 b- stor 19-Jan-10 12:27 36287554/folder_c/
-rw-r-----  2.0 unx        0 b- stor 19-Jan-10 12:23 36287554/file_b
drwxrwx---  2.0 unx        0 b- stor 19-Jan-10 12:27 36287554/folder_b/
drwx------  2.0 unx        0 b- stor 19-Jan-10 12:27 36287554/folder_a/
-rw-r--r--  2.0 unx        0 b- stor 19-Jan-10 12:23 36287554/file_c
7 files, 0 bytes uncompressed, 0 bytes compressed:  0.0%
root@demo:~# cat 36287554.php
<?php
$templateArchive = new ZipArchive();
$templateArchive->open('36287554.zip', ZipArchive::CREATE | ZipArchive::OVERWRITE);

$files = new RecursiveIteratorIterator(
        new RecursiveDirectoryIterator('36287554'),
        RecursiveIteratorIterator::LEAVES_ONLY
);

foreach ($files as $name => $file)
{
        // Get real and relative path for current file
        $filePath = $file->getRealPath();

        $relativePath = $name;

        // Add regular files
        if (!$file->isDir())
        {
                // Add current file to archive
                $templateArchive->addFile($filePath, $relativePath);
        }
        elseif (substr($relativePath, -2) === "/.")
        {
                // Remove the dot representing the current directory
                $relativePath = substr($relativePath, 0, -1);
                // Add current directory to archive
                $templateArchive->addEmptyDir($relativePath);
        }
        else
        {
                continue;
        }

        $templateArchive->setExternalAttributesName($relativePath,
                ZipArchive::OPSYS_UNIX,
                fileperms($filePath) << 16);
}

// Zip archive will be created only after closing object
$templateArchive->close();