Description:
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RecursiveDirectoryIterator() with RecursiveIteratorIterator() not sorting all values by name like on Windows. Try script below on Windows and Linux. This should be sorted by default by name folder and subfolder then next filename. Fix this. I tessted this on PHP 5.5.24 Linux and 5.4.8 Linux and 5.6.11 Windows

Test script:
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<?php
$MójFolder = __DIR__;
$Pliki = array('Pliki'=>array(), 'Foldery'=>array());

$SkanerKatalogówIPlików = new RecursiveDirectoryIterator($MójFolder, RecursiveDirectoryIterator::SKIP_DOTS);
$SkanujWszystkiePodkatalogi = new RecursiveIteratorIterator($SkanerKatalogówIPlików, RecursiveIteratorIterator::SELF_FIRST);

foreach($SkanujWszystkiePodkatalogi as $WszystkiePlikiIFoldery){

    if($WszystkiePlikiIFoldery->isDir()){
        $Pliki['Foldery'][] = $WszystkiePlikiIFoldery .'/';
    }elseif($WszystkiePlikiIFoldery->isFile()){
        $Pliki['Pliki'][] = $WszystkiePlikiIFoldery->getPathname();
    }
}

#print_r($Pliki);

return $Pliki;

Expected result:
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Add sorting by name example:
folder/subfolder1/filename.php
folder/subfolder1/filename1.php